PDBx ontology The PDBx OWL ontology translated from the PDBML schema. PDBID PDB ID for annotating triples CategoryGroup Abstract class for category groups. CategoryGroupElement Abstract class for category group elements. Category Abstract class for category holders. CategoryElement Abstract class for category elements. 1 categoryItem Abstract Datatype property for category items Abstract property for cross-references within PDBML. Abstract property for cross-references between categories. Abstract property for cross-references between categories. Abstract property for external links Abstract property for external RDF links Abstract property for external HTML links link to related PDB entry link to split PDB entry external link to pubmed external link to sequence databases external link to UniProt external link to Bio2RDF PDB entry external link to GenBank external link to EMBL external link to DOI (digital object identifier) external link to NCBI taxonomy external link to NCBI taxonomy (source organism) external link to NCBI taxonomy (host organism) external link to enzyme code external link to gene ontology external link to mmCIF chemical component datablock DATABLOCK class holds all categories of PDB data. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 Abstract property pointing to xxxCategory. Abstract property for xxxCategory. of_datablock Link to the base datablock of category elements of_category Link to the category element holder to which the category element belong 0 atom_site Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_siteCategory> <PDBx:atom_site id="1"> <PDBx:B_iso_or_equiv>17.93</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.369</PDBx:Cartn_x> <PDBx:Cartn_y>30.691</PDBx:Cartn_y> <PDBx:Cartn_z>11.795</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="2"> <PDBx:B_iso_or_equiv>17.75</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.970</PDBx:Cartn_x> <PDBx:Cartn_y>31.965</PDBx:Cartn_y> <PDBx:Cartn_z>12.332</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="3"> <PDBx:B_iso_or_equiv>17.83</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.569</PDBx:Cartn_x> <PDBx:Cartn_y>32.010</PDBx:Cartn_y> <PDBx:Cartn_z>13.808</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="4"> <PDBx:B_iso_or_equiv>17.53</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.735</PDBx:Cartn_x> <PDBx:Cartn_y>31.190</PDBx:Cartn_y> <PDBx:Cartn_z>14.167</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="5"> <PDBx:B_iso_or_equiv>17.66</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.379</PDBx:Cartn_x> <PDBx:Cartn_y>33.146</PDBx:Cartn_y> <PDBx:Cartn_z>11.540</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="6"> <PDBx:B_iso_or_equiv>18.86</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.584</PDBx:Cartn_x> <PDBx:Cartn_y>33.034</PDBx:Cartn_y> <PDBx:Cartn_z>10.030</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="7"> <PDBx:B_iso_or_equiv>17.12</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.933</PDBx:Cartn_x> <PDBx:Cartn_y>33.309</PDBx:Cartn_y> <PDBx:Cartn_z>11.872</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="8"> <PDBx:B_iso_or_equiv>18.97</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.095</PDBx:Cartn_x> <PDBx:Cartn_y>32.930</PDBx:Cartn_y> <PDBx:Cartn_z>14.590</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="9"> <PDBx:B_iso_or_equiv>19.80</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.734</PDBx:Cartn_x> <PDBx:Cartn_y>32.995</PDBx:Cartn_y> <PDBx:Cartn_z>16.032</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="10"> <PDBx:B_iso_or_equiv>20.92</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.695</PDBx:Cartn_x> <PDBx:Cartn_y>34.106</PDBx:Cartn_y> <PDBx:Cartn_z>16.113</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="11"> <PDBx:B_iso_or_equiv>21.84</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.869</PDBx:Cartn_x> <PDBx:Cartn_y>35.118</PDBx:Cartn_y> <PDBx:Cartn_z>15.421</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="12"> <PDBx:B_iso_or_equiv>20.51</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.911</PDBx:Cartn_x> <PDBx:Cartn_y>33.346</PDBx:Cartn_y> <PDBx:Cartn_z>17.018</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="13"> <PDBx:B_iso_or_equiv>20.29</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.946</PDBx:Cartn_x> <PDBx:Cartn_y>33.921</PDBx:Cartn_y> <PDBx:Cartn_z>16.183</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="14"> <PDBx:B_iso_or_equiv>20.59</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.769</PDBx:Cartn_x> <PDBx:Cartn_y>32.142</PDBx:Cartn_y> <PDBx:Cartn_z>17.103</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="15"> <PDBx:B_iso_or_equiv>20.47</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.418</PDBx:Cartn_x> <PDBx:Cartn_y>32.181</PDBx:Cartn_y> <PDBx:Cartn_z>17.878</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="16"> <PDBx:B_iso_or_equiv>20.00</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.489</PDBx:Cartn_x> <PDBx:Cartn_y>33.778</PDBx:Cartn_y> <PDBx:Cartn_z>18.426</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="17"> <PDBx:B_iso_or_equiv>22.08</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.664</PDBx:Cartn_x> <PDBx:Cartn_y>33.855</PDBx:Cartn_y> <PDBx:Cartn_z>16.884</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="18"> <PDBx:B_iso_or_equiv>23.44</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>22.623</PDBx:Cartn_x> <PDBx:Cartn_y>34.850</PDBx:Cartn_y> <PDBx:Cartn_z>17.093</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="19"> <PDBx:B_iso_or_equiv>25.77</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>22.657</PDBx:Cartn_x> <PDBx:Cartn_y>35.113</PDBx:Cartn_y> <PDBx:Cartn_z>18.610</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="20"> <PDBx:B_iso_or_equiv>26.28</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.123</PDBx:Cartn_x> <PDBx:Cartn_y>34.250</PDBx:Cartn_y> <PDBx:Cartn_z>19.406</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="21"> <PDBx:B_iso_or_equiv>22.67</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>21.236</PDBx:Cartn_x> <PDBx:Cartn_y>34.463</PDBx:Cartn_y> <PDBx:Cartn_z>16.492</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="22"> <PDBx:B_iso_or_equiv>22.14</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>20.478</PDBx:Cartn_x> <PDBx:Cartn_y>33.469</PDBx:Cartn_y> <PDBx:Cartn_z>17.371</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="23"> <PDBx:B_iso_or_equiv>21.75</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>21.357</PDBx:Cartn_x> <PDBx:Cartn_y>33.986</PDBx:Cartn_y> <PDBx:Cartn_z>15.016</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="101"> <PDBx:B_iso_or_equiv>17.27</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.171</PDBx:Cartn_x> <PDBx:Cartn_y>29.012</PDBx:Cartn_y> <PDBx:Cartn_z>7.116</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C1</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="102"> <PDBx:B_iso_or_equiv>16.95</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.949</PDBx:Cartn_x> <PDBx:Cartn_y>27.758</PDBx:Cartn_y> <PDBx:Cartn_z>6.793</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C2</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="103"> <PDBx:B_iso_or_equiv>16.85</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.800</PDBx:Cartn_x> <PDBx:Cartn_y>26.678</PDBx:Cartn_y> <PDBx:Cartn_z>7.393</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>O3</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="104"> <PDBx:B_iso_or_equiv>16.43</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>5.930</PDBx:Cartn_x> <PDBx:Cartn_y>27.841</PDBx:Cartn_y> <PDBx:Cartn_z>5.869</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>N4</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> </PDBx:atom_siteCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 atom_siteCategory This property indicates that datablock has a category holder atom_siteCategory. atom_siteCategory This property indicates that atom_siteCategory. has a category atom_site. atom_siteItem Abstract Datatype property for atom_site items. reference_to_atom_site cross-reference to atom_site referenced_by_atom_site cross-reference from atom_site atom_site.B_equiv_geom_mean Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.B_equiv_geom_mean_esd The standard uncertainty (estimated standard deviation) of attribute B_equiv_geom_mean in category atom_site. atom_site.B_iso_or_equiv Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. Note - The particular type of ADP stored in this item is qualified by item attribute pdbx_adp_type. in category refine atom_site.B_iso_or_equiv_esd The standard uncertainty (estimated standard deviation) of attribute B_iso_or_equiv in category atom_site. atom_site.Cartn_x The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. atom_site.Cartn_x_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_x in category atom_site. atom_site.Cartn_y The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. atom_site.Cartn_y_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_y in category atom_site. atom_site.Cartn_z The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. atom_site.Cartn_z_esd The standard uncertainty (estimated standard deviation) of attribute Cartn_z in category atom_site. atom_site.U_equiv_geom_mean Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ atom_site.U_equiv_geom_mean_esd The standard uncertainty (estimated standard deviation) of attribute U_equiv_geom_mean in category atom_site. atom_site.U_iso_or_equiv Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. atom_site.U_iso_or_equiv_esd The standard uncertainty (estimated standard deviation) of attribute U_iso_or_equiv in category atom_site. atom_site.Wyckoff_symbol The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002). Uani Uiso Uovl Umpe Bani Biso Bovl A standard code used to describe the type of atomic displacement parameters used for the site. atom_site.aniso_B11 The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B11_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][1] in category atom_site. atom_site.aniso_B12 The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B12_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][2] in category atom_site. atom_site.aniso_B13 The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B13_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][3] in category atom_site. atom_site.aniso_B22 The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B22_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][2] in category atom_site. atom_site.aniso_B23 The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B23_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][3] in category atom_site. atom_site.aniso_B33 The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site.aniso_B33_esd The standard uncertainty (estimated standard deviation) of attribute aniso_B[3][3] in category atom_site. atom_site.aniso_U11 The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U11_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][1] in category atom_site. atom_site.aniso_U12 The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U12_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][2] in category atom_site. atom_site.aniso_U13 The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U13_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][3] in category atom_site. atom_site.aniso_U22 The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U22_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][2] in category atom_site. atom_site.aniso_U23 The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U23_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][3] in category atom_site. atom_site.aniso_U33 The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site.aniso_U33_esd The standard uncertainty (estimated standard deviation) of attribute aniso_U[3][3] in category atom_site. atom_site.aniso_ratio Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. atom_site.attached_hydrogens The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given. water oxygen 2 hydroxyl oxygen 1 ammonium nitrogen 4 atom_site.auth_asym_id An alternative identifier for attribute label_asym_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. atom_site.auth_atom_id An alternative identifier for attribute label_atom_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. atom_site.auth_comp_id An alternative identifier for attribute label_comp_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. atom_site.auth_seq_id An alternative identifier for attribute label_seq_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of attribute label_seq_id in category atom_site. The value of attribute label_seq_id in category atom_site is required to be a sequential list of positive integers. The author may assign values to attribute auth_seq_id in category atom_site in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. atom_site.calc_attached_atom The attribute id in category atom_site of the atom site to which the 'geometry-calculated' atom site is attached. d calc c dum A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'. atom_site.chemical_conn_number This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. atom_site.constraints A description of the constraints applied to parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_constraints in category refine. pop=1.0-pop(Zn3) atom_site.details A description of special aspects of this site. See also attribute refinement_flags in category atom_site. Ag/Si disordered atom_site.disorder_assembly A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, attribute disorder_group in category atom_site is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** atom_site.disorder_group A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** atom_site.footnote_id The value of attribute footnote_id in category atom_site must match an ID specified by attribute id in category atom_sites_footnote in the ATOM_SITES_FOOTNOTE list. atom_site.fract_x The x coordinate of the atom-site position specified as a fraction of attribute length_a in category cell. atom_site.fract_x_esd The standard uncertainty (estimated standard deviation) of attribute fract_x in category atom_site. atom_site.fract_y The y coordinate of the atom-site position specified as a fraction of attribute length_b in category cell. atom_site.fract_y_esd The standard uncertainty (estimated standard deviation) of attribute fract_y in category atom_site. atom_site.fract_z The z coordinate of the atom-site position specified as a fraction of attribute length_c in category cell. atom_site.fract_z_esd The standard uncertainty (estimated standard deviation) of attribute fract_z in category atom_site. ATOM HETATM The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. atom_site.label_alt_id A component of the identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. atom_site.label_asym_id A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. atom_site.label_atom_id A component of the identifier for this atom site. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. atom_site.label_comp_id A component of the identifier for this atom site. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. atom_site.label_entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. atom_site.label_seq_id This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. atom_site.occupancy_esd The standard uncertainty (estimated standard deviation) of attribute occupancy in category atom_site. atom_site.pdbx_PDB_atom_name PDB atom name. atom_site.pdbx_PDB_ins_code PDB insertion code. atom_site.pdbx_PDB_model_num PDB model number. atom_site.pdbx_PDB_residue_name PDB residue name. atom_site.pdbx_PDB_residue_no PDB residue number. atom_site.pdbx_PDB_strand_id PDB strand id. atom_site.pdbx_auth_alt_id Author's alternate location identifier. atom_site.pdbx_auth_asym_id Author's strand id. atom_site.pdbx_auth_atom_name Author's atom name. atom_site.pdbx_auth_comp_id Author's residue name. atom_site.pdbx_auth_seq_id Author's sequence identifier. atom_site.pdbx_formal_charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 atom_site.pdbx_ncs_dom_id The NCS domain to which the atom position is assigned. The NCS group is defined in category struct_ncs_dom. This item is a reference to attribute id in category struct_ncs_dom. atom_site.pdbx_struct_group_id The value of attribute pdbx_struct_group_id in category atom_site identifies the group or groups assigned to this atom. This is a reference to the identifier for group definition in category PDBX_STRUCT_GROUP_LIST. Multiple groups identifiers are encoded as a comma separated list. atom assigned to individual group C1 C1 atom assigned to multiple groups C1, C2 and C3 C1,C2,C3 atom_site.pdbx_tls_group_id The TLS group to which the atom position is assigned. The TLS group is defined in category pdbx_refine_tls. This item is a reference to attribute id in category pdbx_refine_tls. S G R D T U P A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by attribute refinement_flags_posn in category atom_site, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs. T U TU A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site. P A code which indicates that refinement restraints or constraints were applied to the occupancy of this site. D G R S DG DR DS GR GS RS DGR DGS DRS GRS DGRS A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site. atom_site.restraints A description of restraints applied to specific parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_restraints in category refine. restrained to planar ring atom_site.symmetry_multiplicity The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002). Uani Uiso Uovl Umpe Bani Biso Bovl A standard code used to describe the type of atomic displacement parameters used for the site. atom_site.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. atom_site.id The value of attribute id in category atom_site must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and attribute label_seq_id in category atom_site. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to attribute id in category atom_site. 5 C12 Ca3g28 Fe3+17 H*251 boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0 0 atom_site_anisotrop Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [Acta Cryst. (1985), B41, 255-262]. <PDBx:atom_site_anisotropCategory> <PDBx:atom_site_anisotrop id="1"> <PDBx:U11>8642</PDBx:U11> <PDBx:U12>4866</PDBx:U12> <PDBx:U13>7299</PDBx:U13> <PDBx:U22>-342</PDBx:U22> <PDBx:U23>-258</PDBx:U23> <PDBx:U33>-1427</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="2"> <PDBx:U11>5174</PDBx:U11> <PDBx:U12>4871</PDBx:U12> <PDBx:U13>6243</PDBx:U13> <PDBx:U22>-1885</PDBx:U22> <PDBx:U23>-2051</PDBx:U23> <PDBx:U33>-1377</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="3"> <PDBx:U11>6202</PDBx:U11> <PDBx:U12>5020</PDBx:U12> <PDBx:U13>4395</PDBx:U13> <PDBx:U22>-1130</PDBx:U22> <PDBx:U23>-556</PDBx:U23> <PDBx:U33>-632</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="4"> <PDBx:U11>4224</PDBx:U11> <PDBx:U12>4700</PDBx:U12> <PDBx:U13>5046</PDBx:U13> <PDBx:U22>1105</PDBx:U22> <PDBx:U23>-161</PDBx:U23> <PDBx:U33>345</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="5"> <PDBx:U11>8684</PDBx:U11> <PDBx:U12>4688</PDBx:U12> <PDBx:U13>4171</PDBx:U13> <PDBx:U22>-1850</PDBx:U22> <PDBx:U23>-433</PDBx:U23> <PDBx:U33>-292</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="6"> <PDBx:U11>11226</PDBx:U11> <PDBx:U12>5255</PDBx:U12> <PDBx:U13>3532</PDBx:U13> <PDBx:U22>-341</PDBx:U22> <PDBx:U23>2685</PDBx:U23> <PDBx:U33>1328</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="7"> <PDBx:U11>10214</PDBx:U11> <PDBx:U12>2428</PDBx:U12> <PDBx:U13>5614</PDBx:U13> <PDBx:U22>-2610</PDBx:U22> <PDBx:U23>-1940</PDBx:U23> <PDBx:U33>902</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="8"> <PDBx:U11>4590</PDBx:U11> <PDBx:U12>3488</PDBx:U12> <PDBx:U13>5827</PDBx:U13> <PDBx:U22>751</PDBx:U22> <PDBx:U23>-770</PDBx:U23> <PDBx:U33>986</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="9"> <PDBx:U11>5014</PDBx:U11> <PDBx:U12>4434</PDBx:U12> <PDBx:U13>3447</PDBx:U13> <PDBx:U22>-17</PDBx:U22> <PDBx:U23>-1593</PDBx:U23> <PDBx:U33>539</PDBx:U33> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site_anisotrop> </PDBx:atom_site_anisotropCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 atom_site_anisotropCategory This property indicates that datablock has a category holder atom_site_anisotropCategory. atom_site_anisotropCategory This property indicates that atom_site_anisotropCategory. has a category atom_site_anisotrop. atom_site_anisotropItem Abstract Datatype property for atom_site_anisotrop items. reference_to_atom_site_anisotrop cross-reference to atom_site_anisotrop referenced_by_atom_site_anisotrop cross-reference from atom_site_anisotrop atom_site_anisotrop.B11 The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B11_esd The standard uncertainty (estimated standard deviation) of attribute B[1][1] in category atom_site_anisotrop. atom_site_anisotrop.B12 The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B12_esd The standard uncertainty (estimated standard deviation) of attribute B[1][2] in category atom_site_anisotrop. atom_site_anisotrop.B13 The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B13_esd The standard uncertainty (estimated standard deviation) of attribute B[1][3] in category atom_site_anisotrop. atom_site_anisotrop.B22 The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B22_esd The standard uncertainty (estimated standard deviation) of attribute B[2][2] in category atom_site_anisotrop. atom_site_anisotrop.B23 The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B23_esd The standard uncertainty (estimated standard deviation) of attribute B[2][3] in category atom_site_anisotrop. atom_site_anisotrop.B33 The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. atom_site_anisotrop.B33_esd The standard uncertainty (estimated standard deviation) of attribute B[3][3] in category atom_site_anisotrop. atom_site_anisotrop.U11 The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U11_esd The standard uncertainty (estimated standard deviation) of attribute U[1][1] in category atom_site_anisotrop. atom_site_anisotrop.U12 The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U12_esd The standard uncertainty (estimated standard deviation) of attribute U[1][2] in category atom_site_anisotrop. atom_site_anisotrop.U13 The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U13_esd The standard uncertainty (estimated standard deviation) of attribute U[1][3] in category atom_site_anisotrop. atom_site_anisotrop.U22 The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U22_esd The standard uncertainty (estimated standard deviation) of attribute U[2][2] in category atom_site_anisotrop. atom_site_anisotrop.U23 The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U23_esd The standard uncertainty (estimated standard deviation) of attribute U[2][3] in category atom_site_anisotrop. atom_site_anisotrop.U33 The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. atom_site_anisotrop.U33_esd The standard uncertainty (estimated standard deviation) of attribute U[3][3] in category atom_site_anisotrop. atom_site_anisotrop.pdbx_PDB_ins_code Pointer to attribute pdbx_PDB_ins_code in category atom_site atom_site_anisotrop.pdbx_auth_alt_id Pointer to attribute pdbx_auth_alt_id in category atom_site. atom_site_anisotrop.pdbx_auth_asym_id Pointer to attribute auth_asym_id in category atom_site atom_site_anisotrop.pdbx_auth_atom_id Pointer to attribute auth_atom_id in category atom_site atom_site_anisotrop.pdbx_auth_comp_id Pointer to attribute auth_comp_id in category atom_site atom_site_anisotrop.pdbx_auth_seq_id Pointer to attribute auth_seq_id in category atom_site atom_site_anisotrop.pdbx_label_alt_id Pointer to attribute label_alt_id in category atom_site. atom_site_anisotrop.pdbx_label_asym_id Pointer to attribute label_asym_id in category atom_site atom_site_anisotrop.pdbx_label_atom_id Pointer to attribute label_atom_id in category atom_site atom_site_anisotrop.pdbx_label_comp_id Pointer to attribute label_comp_id in category atom_site atom_site_anisotrop.pdbx_label_seq_id Pointer to attribute label_seq_id in category atom_site atom_site_anisotrop.ratio Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. atom_site_anisotrop.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. atom_site_anisotrop.id This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. 0 atom_sites Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sitesCategory> <PDBx:atom_sites entry_id="5HVP"> <PDBx:Cartn_transf_matrix11>58.39</PDBx:Cartn_transf_matrix11> <PDBx:Cartn_transf_matrix12>0.00</PDBx:Cartn_transf_matrix12> <PDBx:Cartn_transf_matrix13>0.00</PDBx:Cartn_transf_matrix13> <PDBx:Cartn_transf_matrix21>0.00</PDBx:Cartn_transf_matrix21> <PDBx:Cartn_transf_matrix22>86.70</PDBx:Cartn_transf_matrix22> <PDBx:Cartn_transf_matrix23>0.00</PDBx:Cartn_transf_matrix23> <PDBx:Cartn_transf_matrix31>0.00</PDBx:Cartn_transf_matrix31> <PDBx:Cartn_transf_matrix32>0.00</PDBx:Cartn_transf_matrix32> <PDBx:Cartn_transf_matrix33>46.27</PDBx:Cartn_transf_matrix33> <PDBx:Cartn_transf_vector1>0.00</PDBx:Cartn_transf_vector1> <PDBx:Cartn_transf_vector2>0.00</PDBx:Cartn_transf_vector2> <PDBx:Cartn_transf_vector3>0.00</PDBx:Cartn_transf_vector3> <PDBx:Cartn_transform_axes>c along z, astar along x, b along y</PDBx:Cartn_transform_axes> </PDBx:atom_sites> </PDBx:atom_sitesCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 atom_sitesCategory This property indicates that datablock has a category holder atom_sitesCategory. atom_sitesCategory This property indicates that atom_sitesCategory. has a category atom_sites. atom_sitesItem Abstract Datatype property for atom_sites items. reference_to_atom_sites cross-reference to atom_sites referenced_by_atom_sites cross-reference from atom_sites atom_sites.Cartn_transf_matrix11 The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix12 The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix13 The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix21 The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix22 The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix23 The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix31 The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix32 The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_matrix33 The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_vector1 The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_vector2 The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transf_vector3 The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| atom_sites.Cartn_transform_axes A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix attribute Cartn_transf_matrix[][] in category atom_sites. a parallel to x; b in the plane of y and z atom_sites.fract_transf_matrix11 The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix12 The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix13 The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix21 The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix22 The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix23 The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix31 The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix32 The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_matrix33 The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_vector1 The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_vector2 The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| atom_sites.fract_transf_vector3 The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| difmap vecmap heavy direct geom disper isomor This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. *** difmap vecmap heavy direct geom disper isomor This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. *** difmap vecmap heavy direct geom disper isomor This code identifies the method used to locate the non-hydrogen-atom sites not found by attribute solution_primary. in category atom_sites *** This data item would not in general be used in a macromolecular data block. *** atom_sites.special_details Additional information about the atomic coordinates not coded elsewhere in the CIF. atom_sites.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 atom_sites_alt Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_altCategory> <PDBx:atom_sites_alt id="1"> <PDBx:details> Atom sites with the alternative ID set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 2. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 1 correlate with the conformation of the inhibitor marked with alternative ID 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="2"> <PDBx:details> Atom sites with the alternative ID set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 1. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 2 correlate with the conformation of the inhibitor marked with alternative ID 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="3"> <PDBx:details> Atom sites with the alternative ID set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative ID 4. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="4"> <PDBx:details> Atom sites with the alternative ID set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative ID 3. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> </PDBx:atom_sites_altCategory> 0 1 1 atom_sites_altCategory This property indicates that datablock has a category holder atom_sites_altCategory. atom_sites_altCategory This property indicates that atom_sites_altCategory. has a category atom_sites_alt. atom_sites_altItem Abstract Datatype property for atom_sites_alt items. reference_to_atom_sites_alt cross-reference to atom_sites_alt referenced_by_atom_sites_alt cross-reference from atom_sites_alt atom_sites_alt.details A description of special aspects of the modelling of atoms in alternative conformations. atom_sites_alt.id The value of attribute id in category atom_sites_alt must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier. orientation 1 molecule abc 0 atom_sites_alt_ens Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_alt_ensCategory> <PDBx:atom_sites_alt_ens id="Ensemble 1-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 1-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> </PDBx:atom_sites_alt_ensCategory> 0 1 1 atom_sites_alt_ensCategory This property indicates that datablock has a category holder atom_sites_alt_ensCategory. atom_sites_alt_ensCategory This property indicates that atom_sites_alt_ensCategory. has a category atom_sites_alt_ens. atom_sites_alt_ensItem Abstract Datatype property for atom_sites_alt_ens items. reference_to_atom_sites_alt_ens cross-reference to atom_sites_alt_ens referenced_by_atom_sites_alt_ens cross-reference from atom_sites_alt_ens atom_sites_alt_ens.details A description of special aspects of the ensemble structure generated from atoms with various alternative IDs. atom_sites_alt_ens.id The value of attribute id in category atom_sites_alt_ens must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier. 0 atom_sites_alt_gen Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_alt_genCategory> <PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen> </PDBx:atom_sites_alt_genCategory> 1 1 atom_sites_alt_genCategory This property indicates that datablock has a category holder atom_sites_alt_genCategory. atom_sites_alt_genCategory This property indicates that atom_sites_alt_genCategory. has a category atom_sites_alt_gen. atom_sites_alt_genItem Abstract Datatype property for atom_sites_alt_gen items. reference_to_atom_sites_alt_gen cross-reference to atom_sites_alt_gen referenced_by_atom_sites_alt_gen cross-reference from atom_sites_alt_gen atom_sites_alt_gen.alt_id This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. atom_sites_alt_gen.ens_id This data item is a pointer to attribute id in category atom_sites_alt_ens in the ATOM_SITES_ALT_ENS category. 0 atom_sites_footnote Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_footnoteCategory> <PDBx:atom_sites_footnote id="1"> <PDBx:text> The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative IDs *1* and *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="2"> <PDBx:text> Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="3"> <PDBx:text> The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="4"> <PDBx:text> Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="5"> <PDBx:text> The positions of these water molecules correlate with alternative orientations of amino-acid side chains that do not correlate with alternative orientations of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> </PDBx:atom_sites_footnoteCategory> 0 1 1 atom_sites_footnoteCategory This property indicates that datablock has a category holder atom_sites_footnoteCategory. atom_sites_footnoteCategory This property indicates that atom_sites_footnoteCategory. has a category atom_sites_footnote. atom_sites_footnoteItem Abstract Datatype property for atom_sites_footnote items. reference_to_atom_sites_footnote cross-reference to atom_sites_footnote referenced_by_atom_sites_footnote cross-reference from atom_sites_footnote atom_sites_footnote.text The text of the footnote. Footnotes are used to describe an atom site or a group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled. atom_sites_footnote.id A code that identifies the footnote. a b 1 2 0 atom_type Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>2.31000</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>20.8439</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>1.02000</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>10.2075</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.58860</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.568700</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.865000</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>51.6512</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.21560</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>12.2126</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>0.005700</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>3.13220</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>9.89330</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>2.01250</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>28.9975</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>1.16630</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>0.582600</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-11.529</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>3.04850</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>13.2771</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>2.28680</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>5.70110</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.54630</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.323900</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.867000</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>32.9089</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.250800</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="S"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>6.90530</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>1.46790</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>5.20340</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>22.2151</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.43790</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.253600</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>1.58630</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>56.1720</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.866900</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="CL"> <PDBx:oxidation_number>-1</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>18.2915</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>0.006600</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>7.20840</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>1.17170</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>6.53370</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>19.5424</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>2.33860</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>60.4486</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-16.378</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> </PDBx:atom_typeCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:number_in_cell>72</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.009</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.017</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="H"> <PDBx:number_in_cell>100</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>0</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>0</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:number_in_cell>12</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.032</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.047</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:number_in_cell>4</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.018</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.029</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> </PDBx:atom_typeCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 atom_typeCategory This property indicates that datablock has a category holder atom_typeCategory. atom_typeCategory This property indicates that atom_typeCategory. has a category atom_type. atom_typeItem Abstract Datatype property for atom_type items. reference_to_atom_type cross-reference to atom_type referenced_by_atom_type cross-reference from atom_type atom_type.analytical_mass_percent Mass percentage of this atom type derived from chemical analysis. atom_type.description A description of the atom(s) designated by this atom type. In most cases, this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. deuterium 0.34Fe+0.66Ni atom_type.number_in_cell Total number of atoms of this atom type in the unit cell. atom_type.oxidation_number Formal oxidation state of this atom type in the structure. atom_type.radius_bond The effective intramolecular bonding radius in angstroms of this atom type. atom_type.radius_contact The effective intermolecular bonding radius in angstroms of this atom type. atom_type.scat_Cromer_Mann_a1 The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_a2 The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_a3 The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_a4 The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b1 The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b2 The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b3 The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_b4 The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_Cromer_Mann_c The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. atom_type.scat_dispersion_imag The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. atom_type.scat_dispersion_real The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. atom_type.scat_dispersion_source Reference to the source of the real and imaginary dispersion corrections for scattering factors used for this atom type. International Tables Vol. IV Table 2.3.1 atom_type.scat_length_neutron The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. atom_type.scat_source Reference to the source of the scattering factors or scattering lengths used for this atom type. International Tables Vol. IV Table 2.4.6B atom_type.scat_versus_stol_list A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. atom_type.symbol The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. C Cu2+ H(SDS) dummy FeNi 0 audit Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:auditCategory> <PDBx:audit revision_id="1"> <PDBx:creation_date>1992-12-08</PDBx:creation_date> <PDBx:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records</PDBx:creation_method> <PDBx:update_record> 1992-12-09 adjusted to reflect comments from B. McKeever 1992-12-10 adjusted to reflect comments from H. Berman 1992-12-12 adjusted to reflect comments from K. Watenpaugh</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:auditCategory> <PDBx:audit revision_id="2"> <PDBx:creation_date>1991-03-20</PDBx:creation_date> <PDBx:creation_method>from_xtal_archive_file_using_CIFIO</PDBx:creation_method> <PDBx:update_record> 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec&apos;d by co-editor as manuscript HL0007. 1991-04-17 adjustments based on first referee report. 1991-04-18 adjustments based on second referee report.</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> 0 1 0 1 0 1 1 auditCategory This property indicates that datablock has a category holder auditCategory. auditCategory This property indicates that auditCategory. has a category audit. auditItem Abstract Datatype property for audit items. reference_to_audit cross-reference to audit referenced_by_audit cross-reference from audit audit.creation_date A date that the data block was created. The date format is yyyy-mm-dd. 1990-07-12 audit.creation_method A description of how data were entered into the data block. spawned by the program QBEE audit.update_record A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. 1990-07-15 Updated by the Co-editor audit.revision_id The value of attribute revision_id in category audit must uniquely identify a record in the AUDIT list. rev1 0 audit_author Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:audit_authorCategory> <PDBx:audit_author pdbx_ordinal="1"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Fitzgerald, Paula M.D.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="2"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>McKeever, Brian M.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="3"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Van Middlesworth, J.F.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="4"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Springer, James P.</PDBx:name> </PDBx:audit_author> </PDBx:audit_authorCategory> 0 1 1 1 1 audit_authorCategory This property indicates that datablock has a category holder audit_authorCategory. audit_authorCategory This property indicates that audit_authorCategory. has a category audit_author. audit_authorItem Abstract Datatype property for audit_author items. reference_to_audit_author cross-reference to audit_author referenced_by_audit_author cross-reference from audit_author audit_author.address The address of an author of this data block. If there are multiple authors, attribute address in category audit_author is looped with attribute name in category audit_author. Department Institute Street City and postcode COUNTRY audit_author.name The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A audit_author.pdbx_ordinal This data item defines the order of the author's name in the list of audit authors. 1 2 3 0 audit_conform Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. Example 1 - any file conforming to the current CIF core dictionary. <PDBx:audit_conformCategory> <PDBx:audit_conform dict_name="cif_core.dic" dict_version="2.3.1"> <PDBx:dict_location>ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic</PDBx:dict_location> </PDBx:audit_conform> </PDBx:audit_conformCategory> 0 1 1 1 audit_conformCategory This property indicates that datablock has a category holder audit_conformCategory. audit_conformCategory This property indicates that audit_conformCategory. has a category audit_conform. audit_conformItem Abstract Datatype property for audit_conform items. reference_to_audit_conform cross-reference to audit_conform referenced_by_audit_conform cross-reference from audit_conform audit_conform.dict_location A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. audit_conform.dict_name The string identifying the highest-level dictionary defining data names used in this file. audit_conform.dict_version The version number of the dictionary to which the current data block conforms. 0 audit_contact_author Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:audit_contact_authorCategory> <PDBx:audit_contact_author name="Fitzgerald, Paula M.D."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:email>paula_fitzgerald@merck.com</PDBx:email> <PDBx:fax>1(908)5946645</PDBx:fax> <PDBx:phone>1(908)5945510</PDBx:phone> </PDBx:audit_contact_author> </PDBx:audit_contact_authorCategory> 0 1 0 1 0 1 0 1 1 audit_contact_authorCategory This property indicates that datablock has a category holder audit_contact_authorCategory. audit_contact_authorCategory This property indicates that audit_contact_authorCategory. has a category audit_contact_author. audit_contact_authorItem Abstract Datatype property for audit_contact_author items. reference_to_audit_contact_author cross-reference to audit_contact_author referenced_by_audit_contact_author cross-reference from audit_contact_author audit_contact_author.address The mailing address of the author of the data block to whom correspondence should be addressed. Department Institute Street City and postcode COUNTRY audit_contact_author.email The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. name@host.domain.country bm@iucr.org audit_contact_author.fax The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. 12(34)9477334 12()349477334 audit_contact_author.phone The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. 12(34)9477330 12()349477330 12(34)9477330x5543 audit_contact_author.name The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A 0 audit_link Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF. Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. <PDBx:audit_linkCategory> <PDBx:audit_link block_code="morA_pub" block_description="discursive text of paper with two structures"></PDBx:audit_link> <PDBx:audit_link block_code="morA_(1)" block_description="structure 1 of 2"></PDBx:audit_link> <PDBx:audit_link block_code="morA_(2)" block_description="structure 2 of 2"></PDBx:audit_link> </PDBx:audit_linkCategory> Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:audit_linkCategory> <PDBx:audit_link block_code="KSE_PUB" block_description="publication details"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_COM" block_description="experimental data common to ref./mod. structures"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_REF" block_description="reference structure"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_MOD" block_description="modulated structure"></PDBx:audit_link> </PDBx:audit_linkCategory> 1 1 audit_linkCategory This property indicates that datablock has a category holder audit_linkCategory. audit_linkCategory This property indicates that audit_linkCategory. has a category audit_link. audit_linkItem Abstract Datatype property for audit_link items. reference_to_audit_link cross-reference to audit_link referenced_by_audit_link cross-reference from audit_link audit_link.block_code The value of attribute code in category audit_block associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness. audit_link.block_description A textual description of the relationship of the referenced data block to the current one. 0 cell Data items in the CELL category record details about the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:cellCategory> <PDBx:cell entry_id="5HVP"> <PDBx:angle_alpha>90.00</PDBx:angle_alpha> <PDBx:angle_beta>90.00</PDBx:angle_beta> <PDBx:angle_gamma>90.00</PDBx:angle_gamma> <PDBx:details> The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean.</PDBx:details> <PDBx:length_a>58.39</PDBx:length_a> <PDBx:length_a_esd>0.05</PDBx:length_a_esd> <PDBx:length_b>86.70</PDBx:length_b> <PDBx:length_b_esd>0.12</PDBx:length_b_esd> <PDBx:length_c>46.27</PDBx:length_c> <PDBx:length_c_esd>0.06</PDBx:length_c_esd> <PDBx:volume>234237</PDBx:volume> </PDBx:cell> </PDBx:cellCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:cellCategory> <PDBx:cell entry_id="1TOZ"> <PDBx:angle_alpha>90.0</PDBx:angle_alpha> <PDBx:angle_beta>90.0</PDBx:angle_beta> <PDBx:angle_gamma>90.0</PDBx:angle_gamma> <PDBx:length_a>5.959</PDBx:length_a> <PDBx:length_a_esd>0.001</PDBx:length_a_esd> <PDBx:length_b>14.956</PDBx:length_b> <PDBx:length_b_esd>0.001</PDBx:length_b_esd> <PDBx:length_c>19.737</PDBx:length_c> <PDBx:length_c_esd>0.003</PDBx:length_c_esd> <PDBx:volume>1759.0</PDBx:volume> <PDBx:volume_esd>0.3</PDBx:volume_esd> </PDBx:cell> </PDBx:cellCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 cellCategory This property indicates that datablock has a category holder cellCategory. cellCategory This property indicates that cellCategory. has a category cell. cellItem Abstract Datatype property for cell items. reference_to_cell cross-reference to cell referenced_by_cell cross-reference from cell cell.Z_PDB The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. cell.angle_alpha Unit-cell angle alpha of the reported structure in degrees. cell.angle_alpha_esd The standard uncertainty (estimated standard deviation) of attribute angle_alpha in category cell. cell.angle_beta Unit-cell angle beta of the reported structure in degrees. cell.angle_beta_esd The standard uncertainty (estimated standard deviation) of attribute angle_beta in category cell. cell.angle_gamma Unit-cell angle gamma of the reported structure in degrees. cell.angle_gamma_esd The standard uncertainty (estimated standard deviation) of attribute angle_gamma in category cell. cell.details A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c cell.formula_units_Z The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or attribute sum in category chemical_formula. cell.length_a Unit-cell length a corresponding to the structure reported in angstroms. cell.length_a_esd The standard uncertainty (estimated standard deviation) of attribute length_a in category cell. cell.length_b Unit-cell length b corresponding to the structure reported in angstroms. cell.length_b_esd The standard uncertainty (estimated standard deviation) of attribute length_b in category cell. cell.length_c Unit-cell length c corresponding to the structure reported in angstroms. cell.length_c_esd The standard uncertainty (estimated standard deviation) of attribute length_c in category cell. cell.pdbx_unique_axis To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field. cell.reciprocal_angle_alpha The angle (recip-alpha) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_angle_alpha_esd The estimated standard deviation of attribute reciprocal_angle_alpha in category cell. cell.reciprocal_angle_beta The angle (recip-beta) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_angle_beta_esd The estimated standard deviation of attribute reciprocal_angle_beta in category cell. cell.reciprocal_angle_gamma The angle (recip-gamma) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_angle_gamma_esd The estimated standard deviation of attribute reciprocal_angle_gamma in category cell. cell.reciprocal_length_a The reciprocal cell length (recip-a) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_length_a_esd The estimated standard deviation of attribute reciprocal_length_a in category cell. cell.reciprocal_length_b The reciprocal cell length (recip-b) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_length_b_esd The estimated standard deviation of attribute reciprocal_length_b in category cell. cell.reciprocal_length_c The reciprocal cell length (recip-c) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. cell.reciprocal_length_c_esd The estimated standard deviation of attribute reciprocal_length_c in category cell. cell.volume Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = attribute length_a in category cell b = attribute length_b in category cell c = attribute length_c in category cell alpha = attribute angle_alpha in category cell beta = attribute angle_beta in category cell gamma = attribute angle_gamma in category cell cell.volume_esd The standard uncertainty (estimated standard deviation) of attribute volume in category cell. cell.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 cell_measurement Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="5HVP"> <PDBx:temp>293</PDBx:temp> <PDBx:temp_esd>3</PDBx:temp_esd> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:theta_min>11</PDBx:theta_min> <PDBx:wavelength>1.54</PDBx:wavelength> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="1TOZ"> <PDBx:reflns_used>25</PDBx:reflns_used> <PDBx:temp>293</PDBx:temp> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:theta_min>25</PDBx:theta_min> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 cell_measurementCategory This property indicates that datablock has a category holder cell_measurementCategory. cell_measurementCategory This property indicates that cell_measurementCategory. has a category cell_measurement. cell_measurementItem Abstract Datatype property for cell_measurement items. reference_to_cell_measurement cross-reference to cell_measurement referenced_by_cell_measurement cross-reference from cell_measurement cell_measurement.pressure The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). cell_measurement.pressure_esd The standard uncertainty (estimated standard deviation) of attribute pressure in category cell_measurement. cell_measurement.radiation Description of the radiation used to measure the unit-cell data. See also attribute wavelength in category cell_measurement. neutron Cu K\a synchrotron cell_measurement.reflns_used The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. cell_measurement.temp The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). cell_measurement.temp_esd The standard uncertainty (estimated standard deviation) of attribute temp in category cell_measurement. cell_measurement.theta_max The maximum theta angle of reflections used to measure the unit cell in degrees. cell_measurement.theta_min The minimum theta angle of reflections used to measure the unit cell in degrees. cell_measurement.wavelength The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH. cell_measurement.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 cell_measurement_refln Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (unpublished). <PDBx:cell_measurement_reflnCategory> <PDBx:cell_measurement_refln index_h="-2" index_k="4" index_l="1"> <PDBx:theta>8.67</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="3" index_l="2"> <PDBx:theta>9.45</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="3" index_k="0" index_l="2"> <PDBx:theta>9.46</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-3" index_k="4" index_l="1"> <PDBx:theta>8.93</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-2" index_k="1" index_l="-2"> <PDBx:theta>7.53</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="10" index_k="0" index_l="0"> <PDBx:theta>23.77</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="10" index_l="0"> <PDBx:theta>23.78</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-5" index_k="4" index_l="1"> <PDBx:theta>11.14</PDBx:theta> </PDBx:cell_measurement_refln> </PDBx:cell_measurement_reflnCategory> 0 1 1 1 1 cell_measurement_reflnCategory This property indicates that datablock has a category holder cell_measurement_reflnCategory. cell_measurement_reflnCategory This property indicates that cell_measurement_reflnCategory. has a category cell_measurement_refln. cell_measurement_reflnItem Abstract Datatype property for cell_measurement_refln items. reference_to_cell_measurement_refln cross-reference to cell_measurement_refln referenced_by_cell_measurement_refln cross-reference from cell_measurement_refln cell_measurement_refln.theta Theta angle for a reflection used for measurement of the unit cell in degrees. cell_measurement_refln.index_h Miller index h of a reflection used for measurement of the unit cell. cell_measurement_refln.index_k Miller index k of a reflection used for measurement of the unit cell. cell_measurement_refln.index_l Miller index l of a reflection used for measurement of the unit cell. 0 chem_comp Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_compCategory> <PDBx:chem_comp id="phe"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>phenylalanine</PDBx:name> </PDBx:chem_comp> <PDBx:chem_comp id="val"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>alanine</PDBx:name> </PDBx:chem_comp> </PDBx:chem_compCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 chem_compCategory This property indicates that datablock has a category holder chem_compCategory. chem_compCategory This property indicates that chem_compCategory. has a category chem_comp. chem_compItem Abstract Datatype property for chem_comp items. reference_to_chem_comp cross-reference to chem_comp referenced_by_chem_comp cross-reference from chem_comp chem_comp.formula The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S chem_comp.formula_weight Formula mass in daltons of the chemical component. chem_comp.model_details A description of special aspects of the generation of the coordinates for the model of the component. geometry idealized but not minimized chem_comp.model_erf A pointer to an external reference file from which the atomic description of the component is taken. chem_comp.model_source The source of the coordinates for the model of the component. CSD entry ABCDEF built using Quanta/Charmm chem_comp.mon_nstd_class A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer. iodinated base phosphorylated amino acid brominated base modified amino acid glycosylated amino acid chem_comp.mon_nstd_details A description of special details of a nonstandard monomer. no n yes y 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and attribute mon_nstd_details in category chem_comp data items. chem_comp.mon_nstd_parent The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. tyrosine cytosine chem_comp.mon_nstd_parent_comp_id The identifier for the parent component of the nonstandard component. May be be a comma separated list if this component is derived from multiple components. Items in this indirectly point to attribute id in category chem_comp in the CHEM_COMP category. chem_comp.name The full name of the component. alanine valine adenine cytosine chem_comp.number_atoms_all The total number of atoms in the component. chem_comp.number_atoms_nh The number of non-hydrogen atoms in the component. chem_comp.one_letter_code For standard polymer components, the one-letter code for the component. For non-standard polymer components, the one-letter code for parent component if this exists; otherwise, the one-letter code should be given as 'X'. Components that derived from multiple parents components are described by a sequence of one-letter-codes. alanine or adenine A ambiguous asparagine/aspartic acid B arginine R asparagine N aspartic acid D cysteine or cystine or cytosine C glutamine Q glutamic acid E ambiguous glutamine/glutamic acid Z glycine or guanine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P serine S threonine or thymine T tryptophan W tyrosine Y valine V uracil U water O other X chem_comp.pdbx_ambiguous_flag A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous. Software tools may not be able to process this component definition. chem_comp.pdbx_component_no A serial number used by PDB in the FORMUL record. 3 chem_comp.pdbx_formal_charge The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams. chem_comp.pdbx_ideal_coordinates_details This data item identifies the source of the ideal coordinates in the component definition. Y N This data item identifies if ideal coordinates are missing in this definition. chem_comp.pdbx_initial_date Date component was added to database. chem_comp.pdbx_model_coordinates_db_code This data item identifies the PDB database code from which the heavy atom model coordinates were obtained. chem_comp.pdbx_model_coordinates_details This data item provides additional details about the model coordinates in the component definition. Y N This data item identifies if model coordinates are missing in this definition. chem_comp.pdbx_modification_details For nonstandard components a text description of modification of the parent component. ATP chem_comp.pdbx_modified_date Date component was last modified. PDBE PDBJ RCSB This data item identifies the deposition site that processed this chemical component defintion. REL HOLD HPUB OBS DEL REF_ONLY This data item holds the current release status for the component. chem_comp.pdbx_replaced_by Identifies the attribute id in category chem_comp of the component that has replaced this component. q11 tvx chem_comp.pdbx_replaces Identifies the attribute id's in category chem_comp of the components which have been replaced by this component. Multiple id codes should be separated by commas. q11 tvx,atv chem_comp.pdbx_subcomponent_list The list of subcomponents contained in this component. TSM DPH HIS CHF EMR chem_comp.pdbx_synonyms Synonym list for the component. ATP chem_comp.pdbx_type A preliminary classification used by PDB. chem_comp.three_letter_code For standard polymer components, the common three-letter code for the component. Non-standard polymer components and non-polymer components are also assigned three-letter-codes. For ambiguous polymer components three-letter code should be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'. Ambiguous non-polymer components are assigned the code 'UNL'. alanine ALA arginine ARG asparagine ASN aspartic acid ASP ambiguous asparagine/aspartic acid ASX cysteine CYS glutamine GLN glutamic acid GLU glycine GLY ambiguous glutamine/glutamic acid GLX histidine HIS isoleucine ILE leucine LEU lysine LYS methionine MET phenylalanine PHE proline PRO serine SER threonine THR tryptophan TRP tyrosine TRY valine VAL 1-methyladenosine 1MA 5-methylcytosine 5MC 2(prime)-O-methylcytodine OMC 1-methylguanosine 1MG N(2)-methylguanosine 2MG N(2)-dimethylguanosine M2G 7-methylguanosine 7MG 2(prime)-O-methylguanosine 0MG dihydrouridine H2U ribosylthymidine 5MU pseudouridine PSU acetic acid ACE formic acid FOR water HOH other UNK D-peptide linking L-peptide linking D-peptide NH3 amino terminus L-peptide NH3 amino terminus D-peptide COOH carboxy terminus L-peptide COOH carboxy terminus DNA linking RNA linking L-RNA linking L-DNA linking DNA OH 5 prime terminus RNA OH 5 prime terminus DNA OH 3 prime terminus RNA OH 3 prime terminus D-saccharide 1,4 and 1,4 linking L-saccharide 1,4 and 1,4 linking D-saccharide 1,4 and 1,6 linking L-saccharide 1,4 and 1,6 linking L-saccharide D-saccharide saccharide non-polymer peptide linking peptide-like L-gamma-peptide, C-delta linking D-gamma-peptide, C-delta linking L-beta-peptide, C-gamma linking D-beta-peptide, C-gamma linking other For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. chem_comp.id The value of attribute id in category chem_comp must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. ALA VAL DG C 0 chem_comp_angle Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_angleCategory> <PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="PHE"> <PDBx:value_angle>110.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="CB" comp_id="PHE"> <PDBx:value_angle>110.1</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="CB" comp_id="PHE"> <PDBx:value_angle>110.3</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="HA" comp_id="PHE"> <PDBx:value_angle>108.3</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="PHE"> <PDBx:value_angle>118.4</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="OXT" comp_id="PHE"> <PDBx:value_angle>117.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG" comp_id="PHE"> <PDBx:value_angle>114.0</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="O" atom_id_2="C" atom_id_3="OXT" comp_id="PHE"> <PDBx:value_angle>123.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1" comp_id="PHE"> <PDBx:value_angle>120.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2" comp_id="PHE"> <PDBx:value_angle>120.5</PDBx:value_angle> </PDBx:chem_comp_angle> </PDBx:chem_comp_angleCategory> 0 1 0 1 0 1 0 1 1 1 1 1 chem_comp_angleCategory This property indicates that datablock has a category holder chem_comp_angleCategory. chem_comp_angleCategory This property indicates that chem_comp_angleCategory. has a category chem_comp_angle. chem_comp_angleItem Abstract Datatype property for chem_comp_angle items. reference_to_chem_comp_angle cross-reference to chem_comp_angle referenced_by_chem_comp_angle cross-reference from chem_comp_angle chem_comp_angle.value_angle The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. chem_comp_angle.value_angle_esd The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_comp_angle. chem_comp_angle.value_dist The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. chem_comp_angle.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. chem_comp_angle.atom_id_1 The ID of the first of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_angle.atom_id_2 The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_angle.atom_id_3 The ID of the third of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_angle.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_atom Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_atomCategory> <PDBx:chem_comp_atom atom_id="N" comp_id="phe"> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CA" comp_id="phe"> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="C" comp_id="phe"> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="O" comp_id="phe"> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CB" comp_id="phe"> <PDBx:model_Cartn_x>0.00662</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-1.03603</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.11081</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG" comp_id="phe"> <PDBx:model_Cartn_x>0.03254</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.49711</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.50951</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CD1" comp_id="phe"> <PDBx:model_Cartn_x>-1.15813</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.12084</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.13467</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CE1" comp_id="phe"> <PDBx:model_Cartn_x>-1.15720</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.38038</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.42732</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CZ" comp_id="phe"> <PDBx:model_Cartn_x>0.05385</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.51332</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>5.11032</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CE2" comp_id="phe"> <PDBx:model_Cartn_x>1.26137</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.11613</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.50975</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CD2" comp_id="phe"> <PDBx:model_Cartn_x>1.23668</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.38351</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.20288</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="N" comp_id="val"> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CA" comp_id="val"> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="C" comp_id="val"> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="O" comp_id="val"> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CB" comp_id="val"> <PDBx:model_Cartn_x>0.05260</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.99339</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.17429</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG1" comp_id="val"> <PDBx:model_Cartn_x>-0.13288</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.31545</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.52668</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG2" comp_id="val"> <PDBx:model_Cartn_x>-0.94265</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-2.12930</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.99811</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> </PDBx:chem_comp_atomCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 chem_comp_atomCategory This property indicates that datablock has a category holder chem_comp_atomCategory. chem_comp_atomCategory This property indicates that chem_comp_atomCategory. has a category chem_comp_atom. chem_comp_atomItem Abstract Datatype property for chem_comp_atom items. reference_to_chem_comp_atom cross-reference to chem_comp_atom referenced_by_chem_comp_atom cross-reference from chem_comp_atom chem_comp_atom.alt_atom_id An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. chem_comp_atom.charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 chem_comp_atom.model_Cartn_x The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. chem_comp_atom.model_Cartn_x_esd The standard uncertainty (estimated standard deviation) of attribute model_Cartn_x in category chem_comp_atom. chem_comp_atom.model_Cartn_y The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. chem_comp_atom.model_Cartn_y_esd The standard uncertainty (estimated standard deviation) of attribute model_Cartn_y in category chem_comp_atom. chem_comp_atom.model_Cartn_z The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. chem_comp_atom.model_Cartn_z_esd The standard uncertainty (estimated standard deviation) of attribute model_Cartn_z in category chem_comp_atom. chem_comp_atom.partial_charge The partial charge assigned to this atom. chem_comp_atom.pdbx_align Atom name alignment offset in PDB atom field. chem_comp_atom.pdbx_alt_atom_id An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. chem_comp_atom.pdbx_alt_comp_id An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. Y N A flag indicating an aromatic atom. chem_comp_atom.pdbx_component_atom_id The atom identifier in the subcomponent where a larger component has been divided subcomponents. CB CA CG chem_comp_atom.pdbx_component_comp_id The component identifier for the subcomponent where a larger component has been divided subcomponents. HIS PRO Y N A flag indicating a leaving atom. chem_comp_atom.pdbx_model_Cartn_x_ideal An alternative x component of the coordinates for this atom in this component specified as orthogonal angstroms. chem_comp_atom.pdbx_model_Cartn_y_ideal An alternative y component of the coordinates for this atom in this component specified as orthogonal angstroms. chem_comp_atom.pdbx_model_Cartn_z_ideal An alternative z component of the coordinates for this atom in this component specified as orthogonal angstroms. chem_comp_atom.pdbx_ordinal Ordinal index for the component atom list. R S N The chiral configuration of the atom that is a chiral center. main side base phos sugar none This data item assigns the atom to a substructure of the component, if appropriate. chem_comp_atom.type_symbol The code used to identify the atom species representing this atom type. Normally this code is the element symbol. C N O chem_comp_atom.atom_id The value of attribute atom_id in category chem_comp_atom must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. chem_comp_atom.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_bond Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_bondCategory> <PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="phe"> <PDBx:value_order>doub</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CG" atom_id_2="CD1" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CD1" atom_id_2="CE1" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CE1" atom_id_2="CZ" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CZ" atom_id_2="CE2" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CE2" atom_id_2="CD2" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CD2" atom_id_2="CG" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="val"> <PDBx:value_order>doub</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG1" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG2" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> </PDBx:chem_comp_bondCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 chem_comp_bondCategory This property indicates that datablock has a category holder chem_comp_bondCategory. chem_comp_bondCategory This property indicates that chem_comp_bondCategory. has a category chem_comp_bond. chem_comp_bondItem Abstract Datatype property for chem_comp_bond items. reference_to_chem_comp_bond cross-reference to chem_comp_bond referenced_by_chem_comp_bond cross-reference from chem_comp_bond Y N A flag indicating an aromatic bond. chem_comp_bond.pdbx_ordinal Ordinal index for the component bond list. E Z N Stereochemical configuration across a double bond. chem_comp_bond.value_dist The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. chem_comp_bond.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_bond. sing doub trip quad arom poly delo pi The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. chem_comp_bond.atom_id_1 The ID of the first of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_bond.atom_id_2 The ID of the second of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_bond.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_chir Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_chirCategory> <PDBx:chem_comp_chir comp_id="phe" id="phe1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> <PDBx:chem_comp_chir comp_id="val" id="val1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> </PDBx:chem_comp_chirCategory> 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 chem_comp_chirCategory This property indicates that datablock has a category holder chem_comp_chirCategory. chem_comp_chirCategory This property indicates that chem_comp_chirCategory. has a category chem_comp_chir. chem_comp_chirItem Abstract Datatype property for chem_comp_chir items. reference_to_chem_comp_chir cross-reference to chem_comp_chir referenced_by_chem_comp_chir cross-reference from chem_comp_chir R S The chiral configuration of the atom that is a chiral centre. chem_comp_chir.atom_id The ID of the atom that is a chiral centre. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_chir.number_atoms_all The total number of atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. chem_comp_chir.number_atoms_nh The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. sign nosign A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. chem_comp_chir.volume_three The chiral volume, V~c~, for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product chem_comp_chir.volume_three_esd The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_comp_chir. chem_comp_chir.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_chir.id The value of attribute id in category chem_comp_chir must uniquely identify a record in the CHEM_COMP_CHIR list. 0 chem_comp_chir_atom Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_chir_atomCategory> <PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> </PDBx:chem_comp_chir_atomCategory> 0 1 1 1 1 chem_comp_chir_atomCategory This property indicates that datablock has a category holder chem_comp_chir_atomCategory. chem_comp_chir_atomCategory This property indicates that chem_comp_chir_atomCategory. has a category chem_comp_chir_atom. chem_comp_chir_atomItem Abstract Datatype property for chem_comp_chir_atom items. reference_to_chem_comp_chir_atom cross-reference to chem_comp_chir_atom referenced_by_chem_comp_chir_atom cross-reference from chem_comp_chir_atom chem_comp_chir_atom.dev The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. chem_comp_chir_atom.atom_id The ID of an atom bonded to the chiral atom. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_chir_atom.chir_id This data item is a pointer to attribute id in category chem_comp_chir in the CHEM_COMP_CHIR category. chem_comp_chir_atom.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 0 chem_comp_link Data items in the CHEM_COMP_LINK category give details about the links between chemical components. 0 1 1 1 1 1 1 chem_comp_linkCategory This property indicates that datablock has a category holder chem_comp_linkCategory. chem_comp_linkCategory This property indicates that chem_comp_linkCategory. has a category chem_comp_link. chem_comp_linkItem Abstract Datatype property for chem_comp_link items. reference_to_chem_comp_link cross-reference to chem_comp_link referenced_by_chem_comp_link cross-reference from chem_comp_link chem_comp_link.details A description of special aspects of a link between chemical components in the structure. chem_comp_link.type_comp_1 The type of the first of the two components joined by the link. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. chem_comp_link.type_comp_2 The type of the second of the two components joined by the link. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. chem_comp_link.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_comp_plane Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_planeCategory> <PDBx:chem_comp_plane comp_id="phe" id="phe1"></PDBx:chem_comp_plane> </PDBx:chem_comp_planeCategory> 0 1 0 1 1 1 chem_comp_planeCategory This property indicates that datablock has a category holder chem_comp_planeCategory. chem_comp_planeCategory This property indicates that chem_comp_planeCategory. has a category chem_comp_plane. chem_comp_planeItem Abstract Datatype property for chem_comp_plane items. reference_to_chem_comp_plane cross-reference to chem_comp_plane referenced_by_chem_comp_plane cross-reference from chem_comp_plane chem_comp_plane.number_atoms_all The total number of atoms in the plane. chem_comp_plane.number_atoms_nh The number of non-hydrogen atoms in the plane. chem_comp_plane.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_plane.id The value of attribute id in category chem_comp_plane must uniquely identify a record in the CHEM_COMP_PLANE list. 0 chem_comp_plane_atom Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_plane_atomCategory> <PDBx:chem_comp_plane_atom atom_id="CB" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CG" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CD1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CE1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CZ" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CE2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CD2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> </PDBx:chem_comp_plane_atomCategory> 0 1 1 1 1 chem_comp_plane_atomCategory This property indicates that datablock has a category holder chem_comp_plane_atomCategory. chem_comp_plane_atomCategory This property indicates that chem_comp_plane_atomCategory. has a category chem_comp_plane_atom. chem_comp_plane_atomItem Abstract Datatype property for chem_comp_plane_atom items. reference_to_chem_comp_plane_atom cross-reference to chem_comp_plane_atom referenced_by_chem_comp_plane_atom cross-reference from chem_comp_plane_atom chem_comp_plane_atom.dist_esd This data item is the standard deviation of the out-of-plane distance for this atom. chem_comp_plane_atom.atom_id The ID of an atom involved in the plane. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_plane_atom.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_plane_atom.plane_id This data item is a pointer to attribute id in category chem_comp_plane in the CHEM_COMP_PLANE category. 0 chem_comp_tor Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_torCategory> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi1"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>CA</PDBx:atom_id_2> <PDBx:atom_id_3>CB</PDBx:atom_id_3> <PDBx:atom_id_4>CG</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi2"> <PDBx:atom_id_1>CA</PDBx:atom_id_1> <PDBx:atom_id_2>CB</PDBx:atom_id_2> <PDBx:atom_id_3>CG</PDBx:atom_id_3> <PDBx:atom_id_4>CD1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring1"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD1</PDBx:atom_id_3> <PDBx:atom_id_4>CE1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring2"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD2</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring3"> <PDBx:atom_id_1>CG</PDBx:atom_id_1> <PDBx:atom_id_2>CD1</PDBx:atom_id_2> <PDBx:atom_id_3>CE1</PDBx:atom_id_3> <PDBx:atom_id_4>CZ</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring4"> <PDBx:atom_id_1>CD1</PDBx:atom_id_1> <PDBx:atom_id_2>CE1</PDBx:atom_id_2> <PDBx:atom_id_3>CZ</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring5"> <PDBx:atom_id_1>CE1</PDBx:atom_id_1> <PDBx:atom_id_2>CZ</PDBx:atom_id_2> <PDBx:atom_id_3>CE2</PDBx:atom_id_3> <PDBx:atom_id_4>CD2</PDBx:atom_id_4> </PDBx:chem_comp_tor> </PDBx:chem_comp_torCategory> 1 1 1 1 1 1 1 1 1 1 chem_comp_torCategory This property indicates that datablock has a category holder chem_comp_torCategory. chem_comp_torCategory This property indicates that chem_comp_torCategory. has a category chem_comp_tor. chem_comp_torItem Abstract Datatype property for chem_comp_tor items. reference_to_chem_comp_tor cross-reference to chem_comp_tor referenced_by_chem_comp_tor cross-reference from chem_comp_tor chem_comp_tor.atom_id_1 The ID of the first of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.atom_id_2 The ID of the second of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.atom_id_3 The ID of the third of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.atom_id_4 The ID of the fourth of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor.comp_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. chem_comp_tor.id The value of attribute id in category chem_comp_tor must uniquely identify a record in the CHEM_COMP_TOR list. 0 chem_comp_tor_value Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_tor_valueCategory> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>-60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.72</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <PDBx:angle>90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <PDBx:angle>-90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring1"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring2"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring3"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring4"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring5"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> </PDBx:chem_comp_tor_valueCategory> 1 1 1 1 0 1 0 1 1 1 chem_comp_tor_valueCategory This property indicates that datablock has a category holder chem_comp_tor_valueCategory. chem_comp_tor_valueCategory This property indicates that chem_comp_tor_valueCategory. has a category chem_comp_tor_value. chem_comp_tor_valueItem Abstract Datatype property for chem_comp_tor_value items. reference_to_chem_comp_tor_value cross-reference to chem_comp_tor_value referenced_by_chem_comp_tor_value cross-reference from chem_comp_tor_value chem_comp_tor_value.angle A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. chem_comp_tor_value.angle_esd The standard uncertainty (estimated standard deviation) of attribute angle in category chem_comp_tor_value. chem_comp_tor_value.dist A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. chem_comp_tor_value.dist_esd The standard uncertainty (estimated standard deviation) of attribute dist in category chem_comp_tor_value. chem_comp_tor_value.comp_id This data item is a pointer to attribute comp_id in category chem_comp_atom in the CHEM_COMP_ATOM category. chem_comp_tor_value.tor_id This data item is a pointer to attribute id in category chem_comp_tor in the CHEM_COMP_TOR category. 0 chem_link Data items in the CHEM_LINK category give details about the links between chemical components. 0 1 1 chem_linkCategory This property indicates that datablock has a category holder chem_linkCategory. chem_linkCategory This property indicates that chem_linkCategory. has a category chem_link. chem_linkItem Abstract Datatype property for chem_link items. reference_to_chem_link cross-reference to chem_link referenced_by_chem_link cross-reference from chem_link chem_link.details A description of special aspects of a link between chemical components in the structure. chem_link.id The value of attribute id in category chem_link must uniquely identify each item in the CHEM_LINK list. peptide oligosaccharide 1,4 DNA 0 chem_link_angle Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <PDBx:chem_link_angleCategory> <PDBx:chem_link_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> <PDBx:value_angle>111.2</PDBx:value_angle> <PDBx:value_angle_esd>2.8</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> <PDBx:value_angle>120.8</PDBx:value_angle> <PDBx:value_angle_esd>1.7</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>116.2</PDBx:value_angle> <PDBx:value_angle_esd>2.0</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="O" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>123.0</PDBx:value_angle> <PDBx:value_angle_esd>1.6</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="C" atom_id_2="N" atom_id_3="CA" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>121.7</PDBx:value_angle> <PDBx:value_angle_esd>1.8</PDBx:value_angle_esd> </PDBx:chem_link_angle> </PDBx:chem_link_angleCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 chem_link_angleCategory This property indicates that datablock has a category holder chem_link_angleCategory. chem_link_angleCategory This property indicates that chem_link_angleCategory. has a category chem_link_angle. chem_link_angleItem Abstract Datatype property for chem_link_angle items. reference_to_chem_link_angle cross-reference to chem_link_angle referenced_by_chem_link_angle cross-reference from chem_link_angle 1 2 This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. chem_link_angle.value_angle The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. chem_link_angle.value_angle_esd The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_link_angle. chem_link_angle.value_dist The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. chem_link_angle.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. chem_link_angle.atom_id_1 The ID of the first of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_1_comp_id) in category chem_comp_angle. chem_link_angle.atom_id_2 The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_2_comp_id) in category chem_comp_angle. chem_link_angle.atom_id_3 The ID of the third of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_3_comp_id) in category chem_comp_angle. chem_link_angle.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_bond Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <PDBx:chem_link_bondCategory> <PDBx:chem_link_bond atom_id_1="N" atom_id_2="CA" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.458</PDBx:value_dist> <PDBx:value_dist_esd>0.019</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="CA" atom_id_2="C" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.525</PDBx:value_dist> <PDBx:value_dist_esd>0.021</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="C" atom_id_2="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:value_dist>1.329</PDBx:value_dist> <PDBx:value_dist_esd>0.014</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="C" atom_id_2="O" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.231</PDBx:value_dist> <PDBx:value_dist_esd>0.020</PDBx:value_dist_esd> </PDBx:chem_link_bond> </PDBx:chem_link_bondCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 chem_link_bondCategory This property indicates that datablock has a category holder chem_link_bondCategory. chem_link_bondCategory This property indicates that chem_link_bondCategory. has a category chem_link_bond. chem_link_bondItem Abstract Datatype property for chem_link_bond items. reference_to_chem_link_bond cross-reference to chem_link_bond referenced_by_chem_link_bond cross-reference from chem_link_bond 1 2 This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link. chem_link_bond.value_dist The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. chem_link_bond.value_dist_esd The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_link_bond. sing doub trip quad arom poly delo pi The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. chem_link_bond.atom_id_1 The ID of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_bond.atom_id_2 The ID of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. chem_link_bond.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_chir Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 chem_link_chirCategory This property indicates that datablock has a category holder chem_link_chirCategory. chem_link_chirCategory This property indicates that chem_link_chirCategory. has a category chem_link_chir. chem_link_chirItem Abstract Datatype property for chem_link_chir items. reference_to_chem_link_chir cross-reference to chem_link_chir referenced_by_chem_link_chir cross-reference from chem_link_chir 1 2 This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link. R S The chiral configuration of the atom that is a chiral centre. chem_link_chir.atom_id The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_chir.number_atoms_all The total number of atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. chem_link_chir.number_atoms_nh The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. sign nosign A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. chem_link_chir.volume_three The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product chem_link_chir.volume_three_esd The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_link_chir. chem_link_chir.id The value of attribute id in category chem_link_chir must uniquely identify a record in the CHEM_LINK_CHIR list. chem_link_chir.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_chir_atom Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components. 0 1 0 1 1 1 chem_link_chir_atomCategory This property indicates that datablock has a category holder chem_link_chir_atomCategory. chem_link_chir_atomCategory This property indicates that chem_link_chir_atomCategory. has a category chem_link_chir_atom. chem_link_chir_atomItem Abstract Datatype property for chem_link_chir_atom items. reference_to_chem_link_chir_atom cross-reference to chem_link_chir_atom referenced_by_chem_link_chir_atom cross-reference from chem_link_chir_atom 1 2 This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the link. chem_link_chir_atom.dev The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. chem_link_chir_atom.atom_id The ID of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_chir_atom.chir_id This data item is a pointer to attribute id in category chem_link_chir in the CHEM_LINK_CHIR category. 0 chem_link_plane Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. 0 1 0 1 1 1 chem_link_planeCategory This property indicates that datablock has a category holder chem_link_planeCategory. chem_link_planeCategory This property indicates that chem_link_planeCategory. has a category chem_link_plane. chem_link_planeItem Abstract Datatype property for chem_link_plane items. reference_to_chem_link_plane cross-reference to chem_link_plane referenced_by_chem_link_plane cross-reference from chem_link_plane chem_link_plane.number_atoms_all The total number of atoms in the plane. chem_link_plane.number_atoms_nh The number of non-hydrogen atoms in the plane. chem_link_plane.id The value of attribute id in category chem_link_plane must uniquely identify a record in the CHEM_LINK_PLANE list. chem_link_plane.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_plane_atom Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components. 0 1 1 1 chem_link_plane_atomCategory This property indicates that datablock has a category holder chem_link_plane_atomCategory. chem_link_plane_atomCategory This property indicates that chem_link_plane_atomCategory. has a category chem_link_plane_atom. chem_link_plane_atomItem Abstract Datatype property for chem_link_plane_atom items. reference_to_chem_link_plane_atom cross-reference to chem_link_plane_atom referenced_by_chem_link_plane_atom cross-reference from chem_link_plane_atom 1 2 This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the link. chem_link_plane_atom.atom_id The ID of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_plane_atom.plane_id This data item is a pointer to attribute id in category chem_link_plane in the CHEM_LINK_PLANE category. 0 chem_link_tor Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. 0 1 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 chem_link_torCategory This property indicates that datablock has a category holder chem_link_torCategory. chem_link_torCategory This property indicates that chem_link_torCategory. has a category chem_link_tor. chem_link_torItem Abstract Datatype property for chem_link_tor items. reference_to_chem_link_tor cross-reference to chem_link_tor referenced_by_chem_link_tor cross-reference from chem_link_tor 1 2 This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. 1 2 This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link. chem_link_tor.atom_id_1 The ID of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.atom_id_2 The ID of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.atom_id_3 The ID of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.atom_id_4 The ID of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. chem_link_tor.id The value of attribute id in category chem_link_tor must uniquely identify a record in the CHEM_LINK_TOR list. chem_link_tor.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 chem_link_tor_value Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. 1 1 1 1 0 1 0 1 1 chem_link_tor_valueCategory This property indicates that datablock has a category holder chem_link_tor_valueCategory. chem_link_tor_valueCategory This property indicates that chem_link_tor_valueCategory. has a category chem_link_tor_value. chem_link_tor_valueItem Abstract Datatype property for chem_link_tor_value items. reference_to_chem_link_tor_value cross-reference to chem_link_tor_value referenced_by_chem_link_tor_value cross-reference from chem_link_tor_value chem_link_tor_value.angle A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. chem_link_tor_value.angle_esd The standard uncertainty (estimated standard deviation) of attribute angle in category chem_link_tor_value. chem_link_tor_value.dist A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. chem_link_tor_value.dist_esd The standard uncertainty (estimated standard deviation) of attribute dist in category chem_link_tor_value. chem_link_tor_value.tor_id This data item is a pointer to attribute id in category chem_link_tor in the CHEM_LINK_TOR category. 0 chemical Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. <PDBx:chemicalCategory> <PDBx:chemical entry_id="9597gaus"> <PDBx:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</PDBx:name_systematic> </PDBx:chemical> </PDBx:chemicalCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 chemicalCategory This property indicates that datablock has a category holder chemicalCategory. chemicalCategory This property indicates that chemicalCategory. has a category chemical. chemicalItem Abstract Datatype property for chemical items. reference_to_chemical cross-reference to chemical referenced_by_chemical cross-reference from chemical rm ad rmad syn unk Necessary conditions for the assignment of attribute absolute_configuration in category chemical are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021) chemical.compound_source Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. From Norilsk (USSR) Extracted from the bark of Cinchona Naturalis chemical.melting_point The temperature in kelvins at which the crystalline solid changes to a liquid. chemical.melting_point_gt A temperature in kelvins above which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. attribute melting_point in category chemical should always be used in preference to these two items whenever possible. chemical.melting_point_lt A temperature in kelvins below which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. attribute melting_point in category chemical should always be used in preference to these two items whenever possible. chemical.name_common Trivial name by which the compound is commonly known. 1-bromoestradiol chemical.name_mineral Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also attribute compound_source in category chemical. chalcopyrite chemical.name_structure_type Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. perovskite sphalerite A15 chemical.name_systematic IUPAC or Chemical Abstracts full name of the compound. 1-bromoestra-1,3,5(10)-triene-3,17\b-diol chemical.optical_rotation The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent. [\a]^25^~D~ = +108 (c = 3.42, CHCl~3~) chemical.properties_biological A free-text description of the biological properties of the material. diverse biological activities including use as a laxative and strong antibacterial activity against S. aureus and weak activity against cyclooxygenase-1 (COX-1) antibiotic activity against Bacillus subtilis (ATCC 6051) but no significant activity against Candida albicans (ATCC 14053), Aspergillus flavus (NRRL 6541) and Fusarium verticillioides (NRRL 25457) weakly potent lipoxygenase nonredox inhibitor no influenza A virus sialidase inhibitory and plaque reduction activities low toxicity against Drosophila melanogaster chemical.properties_physical A free-text description of the physical properties of the material. air-sensitive moisture-sensitive hygroscopic deliquescent oxygen-sensitive photo-sensitive pyrophoric semiconductor ferromagnetic at low temperature paramagnetic and thermochromic chemical.temperature_decomposition The temperature in kelvins at which the solid decomposes. 350 chemical.temperature_decomposition_esd The estimated standard deviation of attribute temperature_decomposition in category chemical. chemical.temperature_decomposition_gt A temperature in kelvins above which the solid is known to decompose. attribute temperature_decomposition_gt in category chemical and attribute temperature_decomposition_lt in category chemical allow a range of temperatures to be given. attribute temperature_decomposition in category chemical should always be used in preference to these two items whenever possible. 350 chemical.temperature_decomposition_lt A temperature in kelvins below which the solid is known to decompose. attribute temperature_decomposition_gt in category chemical and attribute temperature_decomposition_lt in category chemical allow a range of temperatures to be given. attribute temperature_decomposition in category chemical should always be used in preference to these two items whenever possible. 350 chemical.temperature_sublimation The temperature in kelvins at which the solid sublimes. 350 chemical.temperature_sublimation_esd The estimated standard deviation of attribute temperature_sublimation in category chemical. chemical.temperature_sublimation_gt A temperature in kelvins above which the solid is known to sublime. attribute temperature_sublimation_gt in category chemical and attribute temperature_sublimation_lt in category chemical allow a range of temperatures to be given. attribute temperature_sublimation in category chemical should always be used in preference to these two items whenever possible. 350 chemical.temperature_sublimation_lt A temperature in kelvins below which the solid is known to sublime. attribute temperature_sublimation_gt in category chemical and attribute temperature_sublimation_lt in category chemical allow a range of temperatures to be given. attribute temperature_sublimation in category chemical should always be used in preference to these two items whenever possible. 350 chemical.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 chemical_conn_atom Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. <PDBx:chemical_conn_atomCategory> <PDBx:chemical_conn_atom number="1"> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="2"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="3"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.14</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="4"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.33</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="5"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="6"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="7"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="8"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="9"> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="10"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="11"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.80</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="12"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.60</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="13"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="14"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="15"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="16"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> </PDBx:chemical_conn_atomCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 chemical_conn_atomCategory This property indicates that datablock has a category holder chemical_conn_atomCategory. chemical_conn_atomCategory This property indicates that chemical_conn_atomCategory. has a category chemical_conn_atom. chemical_conn_atomItem Abstract Datatype property for chemical_conn_atom items. reference_to_chemical_conn_atom cross-reference to chemical_conn_atom referenced_by_chemical_conn_atom cross-reference from chemical_conn_atom chemical_conn_atom.NCA The number of connected atoms excluding terminal hydrogen atoms. chemical_conn_atom.NH The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as attribute attached_hydrogens in category atom_site only if none of the hydrogen atoms appear in the ATOM_SITE list. chemical_conn_atom.charge The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 chemical_conn_atom.display_x The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. chemical_conn_atom.display_y The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. chemical_conn_atom.type_symbol This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. chemical_conn_atom.number The chemical sequence number to be associated with this atom. Within an ATOM_SITE list, this number must match one of the attribute chemical_conn_number in category atom_site values. 0 chemical_conn_bond Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. <PDBx:chemical_conn_bondCategory> <PDBx:chemical_conn_bond atom_1="4" atom_2="1"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="5" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="6" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="7" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="10" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="9"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="10"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="13" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="14" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="15" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="17" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="18" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="19" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="20" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="21" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="22" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="23" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="24" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="25" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="26" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="27" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="28" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="29" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="30" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="31" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="32" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> </PDBx:chemical_conn_bondCategory> 0 1 1 1 chemical_conn_bondCategory This property indicates that datablock has a category holder chemical_conn_bondCategory. chemical_conn_bondCategory This property indicates that chemical_conn_bondCategory. has a category chemical_conn_bond. chemical_conn_bondItem Abstract Datatype property for chemical_conn_bond items. reference_to_chemical_conn_bond cross-reference to chemical_conn_bond referenced_by_chemical_conn_bond cross-reference from chemical_conn_bond sing doub trip quad arom poly delo pi The chemical bond type associated with the connection between the two sites attribute atom_1 in category chemical_conn_bond and attribute atom_2 in category chemical_conn_bond. chemical_conn_bond.atom_1 This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. chemical_conn_bond.atom_2 This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. 0 chemical_formula Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and attribute sum in category chemical_formula. For the data item attribute moiety in category chemical_formula, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see attribute moiety). in category chemical_formula (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for attribute moiety in category chemical_formula formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in attribute structural in category chemical_formula, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:chemical_formulaCategory> <PDBx:chemical_formula entry_id="TOZ"> <PDBx:moiety>C18 H25 N O3</PDBx:moiety> <PDBx:sum>C18 H25 N O3</PDBx:sum> <PDBx:weight>303.40</PDBx:weight> </PDBx:chemical_formula> </PDBx:chemical_formulaCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 chemical_formulaCategory This property indicates that datablock has a category holder chemical_formulaCategory. chemical_formulaCategory This property indicates that chemical_formulaCategory. has a category chemical_formula. chemical_formulaItem Abstract Datatype property for chemical_formula items. reference_to_chemical_formula cross-reference to chemical_formula referenced_by_chemical_formula cross-reference from chemical_formula chemical_formula.analytical Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (estimated standard deviations). Fe2.45(2) Ni1.60(3) S4 chemical_formula.iupac Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. [Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H chemical_formula.moiety Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the CHEMICAL_FORMULA category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. C7 H4 Cl Hg N O3 S C12 H17 N4 O S 1+, C6 H2 N3 O7 1- C12 H16 N2 O6, 5(H2 O1) (Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O) chemical_formula.structural See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site data should not be included in this formula (see also attribute analytical) in category chemical_formula. Ca ((Cl O3)2 O)2 (H2 O)6 (Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2 chemical_formula.sum See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the CHEMICAL_FORMULA category description. Parentheses are not normally used. C18 H19 N7 O8 S chemical_formula.weight Formula mass in daltons. This mass should correspond to the formulae given under attribute structural, in category chemical_formula _chemical_formula.moiety or _chemical_formula.sum and, together with the Z value and cell parameters, should yield the density given as attribute density_diffrn in category exptl_crystal. chemical_formula.weight_meas Formula mass in daltons measured by a non-diffraction experiment. chemical_formula.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 citation Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:citationCategory> <PDBx:citation id="primary"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>yes</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> The publication that directly relates to this coordinate set.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>265</PDBx:journal_volume> <PDBx:page_first>14209</PDBx:page_first> <PDBx:page_last>14219</PDBx:page_last> <PDBx:title> Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.</PDBx:title> <PDBx:year>1990</PDBx:year> </PDBx:citation> <PDBx:citation id="2"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>UK</PDBx:country> <PDBx:details> Determination of the structure of the unliganded enzyme.</PDBx:details> <PDBx:journal_abbrev>Nature</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>NATUAS</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>006</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0028-0836</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>337</PDBx:journal_volume> <PDBx:page_first>615</PDBx:page_first> <PDBx:page_last>619</PDBx:page_last> <PDBx:title> Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> <PDBx:citation id="3"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> Crystallization of the unliganded enzyme.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>1919</PDBx:page_first> <PDBx:page_last>1921</PDBx:page_last> <PDBx:title> Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> <PDBx:citation id="4"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> Expression and purification of the enzyme.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>2307</PDBx:page_first> <PDBx:page_last>2312</PDBx:page_last> <PDBx:title> Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> </PDBx:citationCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 citationCategory This property indicates that datablock has a category holder citationCategory. citationCategory This property indicates that citationCategory. has a category citation. citationItem Abstract Datatype property for citation items. reference_to_citation cross-reference to citation referenced_by_citation cross-reference from citation citation.abstract Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. citation.abstract_id_CAS The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. citation.book_id_ISBN The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. citation.book_publisher The name of the publisher of the citation; relevant for books or book chapters. John Wiley and Sons citation.book_publisher_city The location of the publisher of the citation; relevant for books or book chapters. London citation.book_title The title of the book in which the citation appeared; relevant for books or book chapters. no n yes y attribute coordinate_linkage in category citation states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. citation.country The country of publication; relevant for books and book chapters. citation.database_id_CSD Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. LEKKUH citation.database_id_Medline Accession number used by Medline to categorize a specific bibliographic entry. 89064067 citation.details A description of special aspects of the relationship of the contents of the data block to the literature item cited. citation relates to this precise coordinate set citation relates to earlier low-resolution structure citation relates to further refinement of structure reported in citation 2 citation.journal_abbrev Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. J. Mol. Biol. citation.journal_full Full name of the cited journal; relevant for journal articles. Journal of Molecular Biology citation.journal_id_ASTM The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. citation.journal_id_CSD The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). 0070 citation.journal_id_ISSN The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. citation.journal_issue Issue number of the journal cited; relevant for journal articles. 2 citation.journal_volume Volume number of the journal cited; relevant for journal articles. 174 citation.language Language in which the cited article is written. German citation.page_first The first page of the citation; relevant for journal articles, books and book chapters. citation.page_last The last page of the citation; relevant for journal articles, books and book chapters. citation.pdbx_database_id_DOI Document Object Identifier used by doi.org to uniquely specify bibliographic entry. DOI:10.2345/S1384107697000225 citation.pdbx_database_id_PubMed Ascession number used by PubMed to categorize a specific bibliographic entry. 12627512 citation.title The title of the citation; relevant for journal articles, books and book chapters. Structure of diferric duck ovotransferrin at 2.35 \%A resolution. Y N Flag to indicate that this citation will not be published. citation.year The year of the citation; relevant for journal articles, books and book chapters. 1984 citation.id The value of attribute id in category citation must uniquely identify a record in the CITATION list. The attribute id in category citation 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. primary 1 2 0 citation_author Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:citation_authorCategory> <PDBx:citation_author citation_id="primary" name="Fitzgerald, P.M.D." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="McKeever, B.M." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Van Middlesworth, J.F." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Springer, J.P." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Leu, C.-T." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Herber, W.K." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Dixon, R.A.F." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Darke, P.L." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Navia, M.A." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Fitzgerald, P.M.D." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="McKeever, B.M." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Leu, C.-T." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Herber, W.K." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Sigal, I.S." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Darke, P.L." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Springer, J.P." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="McKeever, B.M." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Navia, M.A." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Fitzgerald, P.M.D." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Springer, J.P." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Leu, C.-T." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Heimbach, J.C." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Herber, W.K." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Sigal, I.S." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Darke, P.L." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Darke, P.L." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Leu, C.-T." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Davis, L.J." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Heimbach, J.C." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Diehl, R.E." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Hill, W.S." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Dixon, R.A.F." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Sigal, I.S." ordinal="8"></PDBx:citation_author> </PDBx:citation_authorCategory> 1 1 1 citation_authorCategory This property indicates that datablock has a category holder citation_authorCategory. citation_authorCategory This property indicates that citation_authorCategory. has a category citation_author. citation_authorItem Abstract Datatype property for citation_author items. reference_to_citation_author cross-reference to citation_author referenced_by_citation_author cross-reference from citation_author citation_author.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. citation_author.name Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A citation_author.ordinal This data item defines the order of the author's name in the list of authors of a citation. 0 citation_editor Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list. Example 1 - hypothetical example. <PDBx:citation_editorCategory> <PDBx:citation_editor citation_id="5" name="McKeever, B.M."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Navia, M.A."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Springer, J.P."></PDBx:citation_editor> </PDBx:citation_editorCategory> 0 1 1 1 citation_editorCategory This property indicates that datablock has a category holder citation_editorCategory. citation_editorCategory This property indicates that citation_editorCategory. has a category citation_editor. citation_editorItem Abstract Datatype property for citation_editor items. reference_to_citation_editor cross-reference to citation_editor referenced_by_citation_editor cross-reference from citation_editor citation_editor.ordinal This data item defines the order of the editor's name in the list of editors of a citation. citation_editor.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. citation_editor.name Names of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A 0 computing Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead. Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. <PDBx:computingCategory> <PDBx:computing entry_id="1ABC"> <PDBx:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</PDBx:cell_refinement> <PDBx:data_collection>CAD-4 (Enraf-Nonius, 1989)</PDBx:data_collection> <PDBx:data_reduction>CFEO (Solans, 1978)</PDBx:data_reduction> <PDBx:molecular_graphics>ORTEPII (Johnson, 1976)</PDBx:molecular_graphics> <PDBx:publication_material>PARST (Nardelli, 1983)</PDBx:publication_material> <PDBx:structure_refinement>SHELXL93 (Sheldrick, 1993)</PDBx:structure_refinement> <PDBx:structure_solution>SHELXS86 (Sheldrick, 1990)</PDBx:structure_solution> </PDBx:computing> </PDBx:computingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 computingCategory This property indicates that datablock has a category holder computingCategory. computingCategory This property indicates that computingCategory. has a category computing. computingItem Abstract Datatype property for computing items. reference_to_computing cross-reference to computing referenced_by_computing cross-reference from computing computing.cell_refinement Software used for cell refinement. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) computing.data_collection Software used for data collection. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) computing.data_reduction Software used for data reduction. Give the program or package name and a brief reference. DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990) computing.molecular_graphics Software used for molecular graphics. Give the program or package name and a brief reference. FRODO (Jones, 1986), ORTEP (Johnson, 1965) computing.pdbx_data_reduction_ds Program/package name for data reduction/data scaling computing.pdbx_data_reduction_ii Program/package name for data reduction/intensity integration software computing.pdbx_structure_refinement_method Program/package name for structure refinement method. computing.publication_material Software used for generating material for publication. Give the program or package name and a brief reference. computing.structure_refinement Software used for refinement of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) X-PLOR (Brunger, 1992) computing.structure_solution Software used for solution of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) computing.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 database Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 databaseCategory This property indicates that datablock has a category holder databaseCategory. databaseCategory This property indicates that databaseCategory. has a category database. databaseItem Abstract Datatype property for database items. reference_to_database cross-reference to database referenced_by_database cross-reference from database database.CSD_history A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD). database.code_CAS The code assigned by Chemical Abstracts. database.code_CSD The code assigned by the Cambridge Structural Database. database.code_ICSD The code assigned by the Inorganic Crystal Structure Database. database.code_MDF The code assigned by the Metals Data File. database.code_NBS The code assigned by the NBS (NIST) Crystal Data Database. database.code_PDB The code assigned by the Protein Data Bank. database.code_PDF The code assigned by the Powder Diffraction File (JCPDS/ICDD). database.code_depnum_ccdc_archive Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. database.code_depnum_ccdc_fiz Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). database.code_depnum_ccdc_journal Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). database.journal_ASTM The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service. database.journal_CSD The journal code used in the Cambridge Structural Database. database.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 database_2 Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_2Category> <PDBx:database_2 database_code="5HVP" database_id="PDB"></PDBx:database_2> </PDBx:database_2Category> 1 1 database_2Category This property indicates that datablock has a category holder database_2Category. database_2Category This property indicates that database_2Category. has a category database_2. database_2Item Abstract Datatype property for database_2 items. reference_to_database_2 cross-reference to database_2 referenced_by_database_2 cross-reference from database_2 database_2.database_code The code assigned by the database identified in attribute database_id in category database_2. 1ABC ABCDEF CAS CSD ICSD MDF NDB NBS PDB PDF RCSB EBI PDBE BMRB An abbreviation that identifies the database. 0 database_PDB_caveat Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. Example 1 - hypothetical example. <PDBx:database_PDB_caveatCategory> <PDBx:database_PDB_caveat id="1"> <PDBx:text> THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</PDBx:text> </PDBx:database_PDB_caveat> <PDBx:database_PDB_caveat id="2"> <PDBx:text> UNCORRECTABLE AT THIS TIME</PDBx:text> </PDBx:database_PDB_caveat> </PDBx:database_PDB_caveatCategory> 0 1 1 database_PDB_caveatCategory This property indicates that datablock has a category holder database_PDB_caveatCategory. database_PDB_caveatCategory This property indicates that database_PDB_caveatCategory. has a category database_PDB_caveat. database_PDB_caveatItem Abstract Datatype property for database_PDB_caveat items. reference_to_database_PDB_caveat cross-reference to database_PDB_caveat referenced_by_database_PDB_caveat cross-reference from database_PDB_caveat database_PDB_caveat.text The full text of the PDB caveat record. database_PDB_caveat.id A unique identifier for the PDB caveat record. 0 database_PDB_matrix The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 database_PDB_matrixCategory This property indicates that datablock has a category holder database_PDB_matrixCategory. database_PDB_matrixCategory This property indicates that database_PDB_matrixCategory. has a category database_PDB_matrix. database_PDB_matrixItem Abstract Datatype property for database_PDB_matrix items. reference_to_database_PDB_matrix cross-reference to database_PDB_matrix referenced_by_database_PDB_matrix cross-reference from database_PDB_matrix database_PDB_matrix.origx11 The [1][1] element of the PDB ORIGX matrix. database_PDB_matrix.origx12 The [1][2] element of the PDB ORIGX matrix. database_PDB_matrix.origx13 The [1][3] element of the PDB ORIGX matrix. database_PDB_matrix.origx21 The [2][1] element of the PDB ORIGX matrix. database_PDB_matrix.origx22 The [2][2] element of the PDB ORIGX matrix. database_PDB_matrix.origx23 The [2][3] element of the PDB ORIGX matrix. database_PDB_matrix.origx31 The [3][1] element of the PDB ORIGX matrix. database_PDB_matrix.origx32 The [3][2] element of the PDB ORIGX matrix. database_PDB_matrix.origx33 The [3][3] element of the PDB ORIGX matrix. database_PDB_matrix.origx_vector1 The [1] element of the PDB ORIGX vector. database_PDB_matrix.origx_vector2 The [2] element of the PDB ORIGX vector. database_PDB_matrix.origx_vector3 The [3] element of the PDB ORIGX vector. database_PDB_matrix.scale11 The [1][1] element of the PDB SCALE matrix. database_PDB_matrix.scale12 The [1][2] element of the PDB SCALE matrix. database_PDB_matrix.scale13 The [1][3] element of the PDB SCALE matrix. database_PDB_matrix.scale21 The [2][1] element of the PDB SCALE matrix. database_PDB_matrix.scale22 The [2][2] element of the PDB SCALE matrix. database_PDB_matrix.scale23 The [2][3] element of the PDB SCALE matrix. database_PDB_matrix.scale31 The [3][1] element of the PDB SCALE matrix. database_PDB_matrix.scale32 The [3][2] element of the PDB SCALE matrix. database_PDB_matrix.scale33 The [3][3] element of the PDB SCALE matrix. database_PDB_matrix.scale_vector1 The [1] element of the PDB SCALE vector. database_PDB_matrix.scale_vector2 The [2] element of the PDB SCALE vector. database_PDB_matrix.scale_vector3 The [3] element of the PDB SCALE vector. database_PDB_matrix.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 database_PDB_remark Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. NOTE: These remark records in this category are not uniformly annotated by the PDB and may not be consistent with nomenclature or labeling used in the entry. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_PDB_remarkCategory> <PDBx:database_PDB_remark id="3"> <PDBx:text> REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE WEIGHTS OF THE CORRESPONDING RESTRAINTS) DISTANCE RESTRAINTS (ANGSTROMS) BOND DISTANCE 0.018(0.020) ANGLE DISTANCE 0.038(0.030) PLANAR 1-4 DISTANCE 0.043(0.040) PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) SINGLE TORSION CONTACT 0.216(0.500) MULTIPLE TORSION CONTACT 0.207(0.500) POSSIBLE HYDROGEN BOND 0.245(0.500) CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) PLANAR (OMEGA) 2.6(3.0) STAGGERED 17.4(15.0) ORTHONORMAL 18.1(20.0)</PDBx:text> </PDBx:database_PDB_remark> <PDBx:database_PDB_remark id="4"> <PDBx:text> THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE THE CHAIN INDICATORS *A* AND *B*.</PDBx:text> </PDBx:database_PDB_remark> </PDBx:database_PDB_remarkCategory> 0 1 1 database_PDB_remarkCategory This property indicates that datablock has a category holder database_PDB_remarkCategory. database_PDB_remarkCategory This property indicates that database_PDB_remarkCategory. has a category database_PDB_remark. database_PDB_remarkItem Abstract Datatype property for database_PDB_remark items. reference_to_database_PDB_remark cross-reference to database_PDB_remark referenced_by_database_PDB_remark cross-reference from database_PDB_remark database_PDB_remark.text The full text of the PDB remark record. database_PDB_remark.id A unique identifier for the PDB remark record. 0 database_PDB_rev Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_PDB_revCategory> <PDBx:database_PDB_rev num="1"> <PDBx:author_name>Fitzgerald, Paula M.D</PDBx:author_name> <PDBx:date>1991-10-15</PDBx:date> <PDBx:date_original>1990-04-30</PDBx:date_original> <PDBx:mod_type>0</PDBx:mod_type> <PDBx:status>full release</PDBx:status> </PDBx:database_PDB_rev> </PDBx:database_PDB_revCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 database_PDB_revCategory This property indicates that datablock has a category holder database_PDB_revCategory. database_PDB_revCategory This property indicates that database_PDB_revCategory. has a category database_PDB_rev. database_PDB_revItem Abstract Datatype property for database_PDB_rev items. reference_to_database_PDB_rev cross-reference to database_PDB_rev referenced_by_database_PDB_rev cross-reference from database_PDB_rev database_PDB_rev.author_name The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A database_PDB_rev.date Date the PDB revision took place. Taken from the REVDAT record. database_PDB_rev.date_original Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record. 1980-08-21 0 1 2 3 4 5 Taken from the REVDAT record. Refer to the Protein Data Bank format description at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html for details. database_PDB_rev.replaced_by The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. database_PDB_rev.replaces The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. in preparation prerelease full release obsolete The status of this revision. database_PDB_rev.num The value of attribute num in category database_PDB_rev must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order. 0 database_PDB_rev_record Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - hypothetical example. <PDBx:database_PDB_rev_recordCategory> <PDBx:database_PDB_rev_record rev_num="1" type="CONECT"> <PDBx:details> Error fix - incorrect connection between atoms 2312 and 2317</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="2" type="MATRIX"> <PDBx:details>For consistency with 1995-08-04 style-guide</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="3" type="ORIGX"> <PDBx:details>Based on new data from author</PDBx:details> </PDBx:database_PDB_rev_record> </PDBx:database_PDB_rev_recordCategory> 0 1 1 1 database_PDB_rev_recordCategory This property indicates that datablock has a category holder database_PDB_rev_recordCategory. database_PDB_rev_recordCategory This property indicates that database_PDB_rev_recordCategory. has a category database_PDB_rev_record. database_PDB_rev_recordItem Abstract Datatype property for database_PDB_rev_record items. reference_to_database_PDB_rev_record cross-reference to database_PDB_rev_record referenced_by_database_PDB_rev_record cross-reference from database_PDB_rev_record database_PDB_rev_record.details A description of special aspects of the revision of records in this PDB entry. Based on new data from author For consistency with 1995-08-04 style-guide For consistency with structural class database_PDB_rev_record.rev_num This data item is a pointer to attribute num in category database_PDB_rev in the DATABASE_PDB_REV category. database_PDB_rev_record.type The types of records that were changed in this revision to a PDB entry. CRYST1 SCALE MTRIX ATOM HETATM 0 database_PDB_tvect The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file. 0 1 0 1 0 1 0 1 1 database_PDB_tvectCategory This property indicates that datablock has a category holder database_PDB_tvectCategory. database_PDB_tvectCategory This property indicates that database_PDB_tvectCategory. has a category database_PDB_tvect. database_PDB_tvectItem Abstract Datatype property for database_PDB_tvect items. reference_to_database_PDB_tvect cross-reference to database_PDB_tvect referenced_by_database_PDB_tvect cross-reference from database_PDB_tvect database_PDB_tvect.details A description of special aspects of this TVECT. database_PDB_tvect.vector1 The [1] element of the PDB TVECT vector. database_PDB_tvect.vector2 The [2] element of the PDB TVECT vector. database_PDB_tvect.vector3 The [3] element of the PDB TVECT vector. database_PDB_tvect.id The value of attribute id in category database_PDB_tvect must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. 0 diffrn Data items in the DIFFRN category record details about the diffraction data and their measurement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrnCategory> <PDBx:diffrn id="Set1"> <PDBx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</PDBx:ambient_environment> <PDBx:ambient_temp>293.0</PDBx:ambient_temp> <PDBx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</PDBx:crystal_support> <PDBx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection</PDBx:crystal_treatment> </PDBx:diffrn> </PDBx:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrnCategory> <PDBx:diffrn id="d1"> <PDBx:ambient_temp>293</PDBx:ambient_temp> <PDBx:details> \q scan width (1.0 + 0.14tan\q)\&#37;, \q scan rate 1.2\&#37; per min. Background counts for 5 sec on each side every scan.</PDBx:details> </PDBx:diffrn> </PDBx:diffrnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 diffrnCategory This property indicates that datablock has a category holder diffrnCategory. diffrnCategory This property indicates that diffrnCategory. has a category diffrn. diffrnItem Abstract Datatype property for diffrn items. reference_to_diffrn cross-reference to diffrn referenced_by_diffrn cross-reference from diffrn diffrn.ambient_environment The gas or liquid surrounding the sample, if not air. diffrn.ambient_pressure The mean hydrostatic pressure in kilopascals at which the intensities were measured. diffrn.ambient_pressure_esd The estimated standard deviation of attribute ambient_pressure in category diffrn. diffrn.ambient_pressure_gt The mean hydrostatic pressure in kilopascals above which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_pressure_lt The mean hydrostatic pressure in kilopascals below which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_temp The mean temperature in kelvins at which the intensities were measured. diffrn.ambient_temp_details A description of special aspects of temperature control during data collection. diffrn.ambient_temp_esd The standard uncertainty (estimated standard deviation) of attribute ambient_temp in category diffrn. diffrn.ambient_temp_gt The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. diffrn.ambient_temp_lt The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. diffrn.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. diffrn.crystal_support The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop diffrn.crystal_treatment Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. equilibrated in hutch for 24 hours flash frozen in liquid nitrogen slow cooled with direct air stream diffrn.details Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. diffrn.id This data item uniquely identifies a set of diffraction data. 0 diffrn_attenuator Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_attenuatorCategory> <PDBx:diffrn_attenuator code="1"> <PDBx:scale>16.976</PDBx:scale> </PDBx:diffrn_attenuator> </PDBx:diffrn_attenuatorCategory> 0 1 0 1 1 diffrn_attenuatorCategory This property indicates that datablock has a category holder diffrn_attenuatorCategory. diffrn_attenuatorCategory This property indicates that diffrn_attenuatorCategory. has a category diffrn_attenuator. diffrn_attenuatorItem Abstract Datatype property for diffrn_attenuator items. reference_to_diffrn_attenuator cross-reference to diffrn_attenuator referenced_by_diffrn_attenuator cross-reference from diffrn_attenuator diffrn_attenuator.material Material from which the attenuator is made. diffrn_attenuator.scale The scale factor applied when an intensity measurement is reduced by an attenuator identified by attribute code. in category diffrn_attenuator The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities. diffrn_attenuator.code A code associated with a particular attenuator setting. This code is referenced by the attribute attenuator_code in category diffrn_refln which is stored with the diffraction data. See attribute scale in category diffrn_attenuator. 0 diffrn_detector Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_detectorCategory> <PDBx:diffrn_detector diffrn_id="d1"> <PDBx:detector>multiwire</PDBx:detector> <PDBx:type>Siemens</PDBx:type> </PDBx:diffrn_detector> </PDBx:diffrn_detectorCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_detectorCategory This property indicates that datablock has a category holder diffrn_detectorCategory. diffrn_detectorCategory This property indicates that diffrn_detectorCategory. has a category diffrn_detector. diffrn_detectorItem Abstract Datatype property for diffrn_detector items. reference_to_diffrn_detector cross-reference to diffrn_detector referenced_by_diffrn_detector cross-reference from diffrn_detector diffrn_detector.area_resol_mean The resolution of an area detector, in pixels/mm. diffrn_detector.details A description of special aspects of the radiation detector. diffrn_detector.detector The general class of the radiation detector. photographic film scintillation counter CCD plate BF~3~ counter diffrn_detector.dtime The deadtime in microseconds of the detector used to measure the diffraction intensities. diffrn_detector.pdbx_collection_date The date of data collection. 1996-12-25 diffrn_detector.pdbx_collection_time_total The total number of seconds required to measure this data set. 120.0 diffrn_detector.pdbx_frames_total The total number of data frames collected for this data set. 20 100 diffrn_detector.type The make, model or name of the detector device used. diffrn_detector.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_measurement Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="d1"> <PDBx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</PDBx:details> <PDBx:device>3-circle camera</PDBx:device> <PDBx:device_details>none</PDBx:device_details> <PDBx:device_type>Supper model x</PDBx:device_type> <PDBx:method>omega scan</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="s1"> <PDBx:device_type>Philips PW1100/20 diffractometer</PDBx:device_type> <PDBx:method>\q/2\q</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_measurementCategory This property indicates that datablock has a category holder diffrn_measurementCategory. diffrn_measurementCategory This property indicates that diffrn_measurementCategory. has a category diffrn_measurement. diffrn_measurementItem Abstract Datatype property for diffrn_measurement items. reference_to_diffrn_measurement cross-reference to diffrn_measurement referenced_by_diffrn_measurement cross-reference from diffrn_measurement diffrn_measurement.details A description of special aspects of the intensity measurement. 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees diffrn_measurement.device The general class of goniometer or device used to support and orient the specimen. 3-circle camera 4-circle camera kappa-geometry camera oscillation camera precession camera diffrn_measurement.device_details A description of special aspects of the device used to measure the diffraction intensities. commercial goniometer modified locally to allow for 90\% \t arc diffrn_measurement.device_type The make, model or name of the measurement device (goniometer) used. Supper model q Huber model r Enraf-Nonius model s homemade diffrn_measurement.method Method used to measure intensities. profile data from theta/2theta scans diffrn_measurement.specimen_support The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop diffrn_measurement.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_orient_matrix Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <PDBx:diffrn_orient_matrixCategory> <PDBx:diffrn_orient_matrix diffrn_id="set1"> <PDBx:UB11>-0.071479</PDBx:UB11> <PDBx:UB12>0.020208</PDBx:UB12> <PDBx:UB13>0.039076</PDBx:UB13> <PDBx:UB21>0.035372</PDBx:UB21> <PDBx:UB22>0.056209</PDBx:UB22> <PDBx:UB23>0.078324</PDBx:UB23> <PDBx:UB31>-0.007470</PDBx:UB31> <PDBx:UB32>0.067854</PDBx:UB32> <PDBx:UB33>-0.017832</PDBx:UB33> <PDBx:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</PDBx:type> </PDBx:diffrn_orient_matrix> </PDBx:diffrn_orient_matrixCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_orient_matrixCategory This property indicates that datablock has a category holder diffrn_orient_matrixCategory. diffrn_orient_matrixCategory This property indicates that diffrn_orient_matrixCategory. has a category diffrn_orient_matrix. diffrn_orient_matrixItem Abstract Datatype property for diffrn_orient_matrix items. reference_to_diffrn_orient_matrix cross-reference to diffrn_orient_matrix referenced_by_diffrn_orient_matrix cross-reference from diffrn_orient_matrix diffrn_orient_matrix.UB11 The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB12 The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB13 The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB21 The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB22 The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB23 The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB31 The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB32 The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.UB33 The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. diffrn_orient_matrix.type A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. diffrn_orient_matrix.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_orient_refln Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <PDBx:diffrn_orient_reflnCategory> <PDBx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <PDBx:angle_chi>-28.45</PDBx:angle_chi> <PDBx:angle_kappa>-11.32</PDBx:angle_kappa> <PDBx:angle_omega>5.33</PDBx:angle_omega> <PDBx:angle_phi>101.78</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>10.66</PDBx:angle_theta> </PDBx:diffrn_orient_refln> </PDBx:diffrn_orient_reflnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 diffrn_orient_reflnCategory This property indicates that datablock has a category holder diffrn_orient_reflnCategory. diffrn_orient_reflnCategory This property indicates that diffrn_orient_reflnCategory. has a category diffrn_orient_refln. diffrn_orient_reflnItem Abstract Datatype property for diffrn_orient_refln items. reference_to_diffrn_orient_refln cross-reference to diffrn_orient_refln referenced_by_diffrn_orient_refln cross-reference from diffrn_orient_refln diffrn_orient_refln.angle_chi Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_kappa Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_omega Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_phi Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_psi Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.angle_theta Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. diffrn_orient_refln.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. diffrn_orient_refln.index_h Miller index h of a reflection used to define the orientation matrix. diffrn_orient_refln.index_k Miller index k of a reflection used to define the orientation matrix. diffrn_orient_refln.index_l Miller index l of a reflection used to define the orientation matrix. 0 diffrn_radiation Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:collimation>0.3 mm double pinhole</PDBx:collimation> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_radiationCategory This property indicates that datablock has a category holder diffrn_radiationCategory. diffrn_radiationCategory This property indicates that diffrn_radiationCategory. has a category diffrn_radiation. diffrn_radiationItem Abstract Datatype property for diffrn_radiation items. reference_to_diffrn_radiation cross-reference to diffrn_radiation referenced_by_diffrn_radiation cross-reference from diffrn_radiation diffrn_radiation.collimation The collimation or focusing applied to the radiation. 0.3 mm double-pinhole 0.5 mm focusing mirrors diffrn_radiation.filter_edge Absorption edge in angstroms of the radiation filter used. diffrn_radiation.inhomogeneity Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. diffrn_radiation.monochromator The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. Zr filter Ge 220 none equatorial mounted graphite diffrn_radiation.pdbx_analyzer Indicates the method used to obtain monochromatic radiation. attribute monochromator in category diffrn_radiation describes the primary beam monochromator (pre-specimen monochromation). attribute pdbx_analyzer in category diffrn_radiation specifies the post-diffraction analyser (post-specimen) monochromation. Note that monochromators may have either 'parallel' or 'antiparallel' orientation. It is assumed that the geometry is parallel unless specified otherwise. In a parallel geometry, the position of the monochromator allows the incident beam and the final post-specimen and post-monochromator beam to be as close to parallel as possible. In a parallel geometry, the diffracting planes in the specimen and monochromator will be parallel when 2*theta(monochromator) is equal to 2*theta (specimen). For further discussion see R. Jenkins and R. Snyder, Introduction to X-ray Powder Diffraction, Wiley (1996), pp. 164-5. GE(111) Zr filter Ge 220 none equatorial mounted graphite (0001) Si (111), antiparallel diffrn_radiation.pdbx_diffrn_protocol SINGLE WAVELENGTH, LAUE, or MAD. SINGLE WAVELENGTH MONOCHROMATIC LAUE MAD OTHER M L Monochromatic or Laue. M L x-ray neutron electron The radiation scattering type for this diffraction data set. diffrn_radiation.pdbx_wavelength Wavelength of radiation. diffrn_radiation.pdbx_wavelength_list Comma separated list of wavelengths or wavelength range. diffrn_radiation.polarisn_norm The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See attribute polarisn_ratio in category diffrn_radiation. diffrn_radiation.polarisn_ratio Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized component of the radiation. The perpendicular component forms an angle of attribute polarisn_norm in category diffrn_radiation to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). x-ray neutron electron gamma The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined. diffrn_radiation.type The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. CuK\a Cu K\a~1~ Cu K-L~2,3~ white-beam diffrn_radiation.wavelength_id This data item is a pointer to attribute id in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category. K-L~3~ K-L~2~ K-M~3~ K-L~2,3~ The IUPAC symbol for the X-ray wavelength for the probe radiation. diffrn_radiation.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_radiation_wavelength Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_radiation_wavelengthCategory> <PDBx:diffrn_radiation_wavelength id="1"> <PDBx:wavelength>1.54</PDBx:wavelength> <PDBx:wt>1.0</PDBx:wt> </PDBx:diffrn_radiation_wavelength> </PDBx:diffrn_radiation_wavelengthCategory> 1 1 0 1 1 diffrn_radiation_wavelengthCategory This property indicates that datablock has a category holder diffrn_radiation_wavelengthCategory. diffrn_radiation_wavelengthCategory This property indicates that diffrn_radiation_wavelengthCategory. has a category diffrn_radiation_wavelength. diffrn_radiation_wavelengthItem Abstract Datatype property for diffrn_radiation_wavelength items. reference_to_diffrn_radiation_wavelength cross-reference to diffrn_radiation_wavelength referenced_by_diffrn_radiation_wavelength cross-reference from diffrn_radiation_wavelength diffrn_radiation_wavelength.wavelength The radiation wavelength in angstroms. diffrn_radiation_wavelength.wt The relative weight of a wavelength identified by the code attribute id in category diffrn_radiation_wavelength in the list of wavelengths. diffrn_radiation_wavelength.id The code identifying each value of attribute wavelength. in category diffrn_radiation_wavelength Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The attribute wavelength_id in category diffrn_refln codes must match one of the codes defined in this category. x1 x2 neut 0 diffrn_refln Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by attribute diffrn_id. in category diffrn_refln The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by attribute diffrn_id in category diffrn_reflns. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102. <PDBx:diffrn_reflnCategory> <PDBx:diffrn_refln diffrn_id="set1" id="1102"> <PDBx:angle_chi>32.21</PDBx:angle_chi> <PDBx:angle_kappa>20.12</PDBx:angle_kappa> <PDBx:angle_omega>11.54</PDBx:angle_omega> <PDBx:angle_phi>176.02</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>23.08</PDBx:angle_theta> <PDBx:attenuator_code>Ni.005</PDBx:attenuator_code> <PDBx:counts_bg_1>22</PDBx:counts_bg_1> <PDBx:counts_bg_2>25</PDBx:counts_bg_2> <PDBx:counts_net>3450</PDBx:counts_net> <PDBx:counts_peak>321</PDBx:counts_peak> <PDBx:counts_total>3499</PDBx:counts_total> <PDBx:detect_slit_horiz>0.04</PDBx:detect_slit_horiz> <PDBx:detect_slit_vert>0.02</PDBx:detect_slit_vert> <PDBx:elapsed_time>1.00</PDBx:elapsed_time> <PDBx:index_h>4</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>2</PDBx:index_l> <PDBx:intensity_net>202.56</PDBx:intensity_net> <PDBx:intensity_sigma>2.18</PDBx:intensity_sigma> <PDBx:scale_group_code>A24</PDBx:scale_group_code> <PDBx:scan_mode>om</PDBx:scan_mode> <PDBx:scan_mode_backgd>mo</PDBx:scan_mode_backgd> <PDBx:scan_rate>1.2</PDBx:scan_rate> <PDBx:scan_time_backgd>900.00</PDBx:scan_time_backgd> <PDBx:scan_width>1.0</PDBx:scan_width> <PDBx:sint_over_lambda>0.25426</PDBx:sint_over_lambda> <PDBx:standard_code>1</PDBx:standard_code> <PDBx:wavelength>1.54184</PDBx:wavelength> <PDBx:wavelength_id>Cu1fixed</PDBx:wavelength_id> </PDBx:diffrn_refln> </PDBx:diffrn_reflnCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 1 1 diffrn_reflnCategory This property indicates that datablock has a category holder diffrn_reflnCategory. diffrn_reflnCategory This property indicates that diffrn_reflnCategory. has a category diffrn_refln. diffrn_reflnItem Abstract Datatype property for diffrn_refln items. reference_to_diffrn_refln cross-reference to diffrn_refln referenced_by_diffrn_refln cross-reference from diffrn_refln diffrn_refln.angle_chi The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_kappa The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_omega The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_phi The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_psi The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.angle_theta The diffractometer angle theta of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. diffrn_refln.attenuator_code The code identifying the attenuator setting for this reflection. This code must match one of the attribute code in category diffrn_attenuator values. diffrn_refln.class_code The code identifying the class to which this reflection has been assigned. This code must match a value of attribute code in category diffrn_reflns_class. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. diffrn_refln.counts_bg_1 The diffractometer counts for the measurement of the background before the peak. diffrn_refln.counts_bg_2 The diffractometer counts for the measurement of the background after the peak. diffrn_refln.counts_net The diffractometer counts for the measurement of net counts after background removal. diffrn_refln.counts_peak The diffractometer counts for the measurement of counts for the peak scan or position. diffrn_refln.counts_total The diffractometer counts for the measurement of total counts (background plus peak). diffrn_refln.detect_slit_horiz Total slit aperture in degrees in the diffraction plane. diffrn_refln.detect_slit_vert Total slit aperture in degrees perpendicular to the diffraction plane. diffrn_refln.elapsed_time Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity. diffrn_refln.index_h Miller index h of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. diffrn_refln.index_k Miller index k of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. diffrn_refln.index_l Miller index l of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. diffrn_refln.intensity_net Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. diffrn_refln.intensity_sigma Standard uncertainty (estimated standard deviation) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. diffrn_refln.intensity_u Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. diffrn_refln.scale_group_code The code identifying the scale applying to this reflection. This data item is a pointer to attribute code in category diffrn_scale_group in the DIFFRN_SCALE_GROUP category. om ot q The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. st mo The code identifying the mode of scanning a reflection to measure the background intensity. diffrn_refln.scan_rate The rate of scanning a reflection in degrees per minute to measure the intensity. diffrn_refln.scan_time_backgd The time spent measuring each background in seconds. diffrn_refln.scan_width The scan width in degrees of the scan mode defined by the code attribute scan_mode in category diffrn_refln. diffrn_refln.sint_over_lambda The (sin theta)/lambda value in reciprocal angstroms for this reflection. diffrn_refln.standard_code The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to attribute code in category diffrn_standard_refln in the DIFFRN_STANDARD_REFLN category. diffrn_refln.wavelength The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. diffrn_refln.wavelength_id This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. diffrn_refln.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. diffrn_refln.id The value of attribute id in category diffrn_refln must uniquely identify the reflection in the data set identified by the item attribute diffrn_id. in category diffrn_refln Note that this item need not be a number; it can be any unique identifier. 0 diffrn_reflns Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_reflnsCategory This property indicates that datablock has a category holder diffrn_reflnsCategory. diffrn_reflnsCategory This property indicates that diffrn_reflnsCategory. has a category diffrn_reflns. diffrn_reflnsItem Abstract Datatype property for diffrn_reflns items. reference_to_diffrn_reflns cross-reference to diffrn_reflns referenced_by_diffrn_reflns cross-reference from diffrn_reflns diffrn_reflns.av_R_equivalents The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average absolute difference between av(I) and the individual symmetry-equivalent intensities. diffrn_reflns.av_sigmaI_over_netI Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. diffrn_reflns.av_unetI_over_netI Measure [sum u(net I)|/sum|net I|] for all measured reflections. diffrn_reflns.limit_h_max The maximum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. diffrn_reflns.limit_h_min The minimum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. diffrn_reflns.limit_k_max The maximum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. diffrn_reflns.limit_k_min The minimum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. diffrn_reflns.limit_l_max The maximum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. diffrn_reflns.limit_l_min The minimum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. diffrn_reflns.number The total number of measured intensities, excluding reflections that are classified as systematically absent. diffrn_reflns.pdbx_Rmerge_I_obs The R factor for merging the reflections that satisfy the resolution limits established by attribute d_resolution_high in category diffrn_reflns and attribute d_resolution_low in category diffrn_reflns and the observation limit established by attribute observed_criterion. in category diffrn_reflns Rmerge(I) = [sum~i~(sum~j~|I~j~ - |)] / [sum~i~(sum~j~)] I~j~ = the intensity of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection diffrn_reflns.pdbx_Rsym_value The R factor for averaging the symmetry related reflections to a unique data set. diffrn_reflns.pdbx_chi_squared Overall Chi-squared statistic for the data set. diffrn_reflns.pdbx_d_res_high The highest resolution for the interplanar spacings in the reflection data set. This is the smallest d value. diffrn_reflns.pdbx_d_res_low The lowest resolution for the interplanar spacings in the reflection data set. This is the largest d value. diffrn_reflns.pdbx_number_obs The number of reflections satisfying the observation criterion as in attribute pdbx_observed_criterion in category diffrn_reflns diffrn_reflns.pdbx_observed_criterion The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. diffrn_reflns.pdbx_percent_possible_obs The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _diffrn_reflns.d_resolution_high and _diffrn_reflns.d_resolution_low and the observation limit established by attribute observed_criterion. in category diffrn_reflns diffrn_reflns.pdbx_redundancy The overall redundancy for the data set. diffrn_reflns.pdbx_rejects The number of rejected reflections in the data set. The reflections may be rejected by setting the observation criterion, attribute observed_criterion in category diffrn_reflns. diffrn_reflns.reduction_process A description of the process used to reduce the intensity data into structure-factor magnitudes. data averaged using Fisher test diffrn_reflns.theta_max Maximum theta angle in degrees for the measured diffraction intensities. diffrn_reflns.theta_min Minimum theta angle in degrees for the measured diffraction intensities. diffrn_reflns.transf_matrix11 The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix12 The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix13 The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix21 The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix22 The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix23 The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix31 The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix32 The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.transf_matrix33 The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. diffrn_reflns.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_reflns_class Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment. Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. <PDBx:diffrn_reflns_classCategory> <PDBx:diffrn_reflns_class code="Main"> <PDBx:av_R_eq>0.015</PDBx:av_R_eq> <PDBx:d_res_high>0.551</PDBx:d_res_high> <PDBx:d_res_low>6.136</PDBx:d_res_low> <PDBx:description>m=0; main reflections</PDBx:description> <PDBx:number>1580</PDBx:number> </PDBx:diffrn_reflns_class> <PDBx:diffrn_reflns_class code="Sat1"> <PDBx:av_R_eq>0.010</PDBx:av_R_eq> <PDBx:d_res_high>0.551</PDBx:d_res_high> <PDBx:d_res_low>6.136</PDBx:d_res_low> <PDBx:description>m=1; first-order satellites</PDBx:description> <PDBx:number>1045</PDBx:number> </PDBx:diffrn_reflns_class> </PDBx:diffrn_reflns_classCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_reflns_classCategory This property indicates that datablock has a category holder diffrn_reflns_classCategory. diffrn_reflns_classCategory This property indicates that diffrn_reflns_classCategory. has a category diffrn_reflns_class. diffrn_reflns_classItem Abstract Datatype property for diffrn_reflns_class items. reference_to_diffrn_reflns_class cross-reference to diffrn_reflns_class referenced_by_diffrn_reflns_class cross-reference from diffrn_reflns_class diffrn_reflns_class.av_R_eq For each reflection class, the residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The av|del(I)| term is the average absolute difference between av(I) and the individual intensities. diffrn_reflns_class.av_sgI_over_I Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities in a reflection class. diffrn_reflns_class.av_uI_over_I Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. diffrn_reflns_class.d_res_high The smallest value in angstroms for the interplanar spacings for the reflections in each measured reflection class. This is called the highest resolution for this reflection class. diffrn_reflns_class.d_res_low The largest value in angstroms of the interplanar spacings for the reflections for each measured reflection class. This is called the lowest resolution for this reflection class. diffrn_reflns_class.description Description of each reflection class. m=1 first order satellites H0L0 common projection reflections diffrn_reflns_class.number The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations. diffrn_reflns_class.code The code identifying a certain reflection class. 1 m1 s2 0 diffrn_scale_group Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <PDBx:diffrn_scale_groupCategory> <PDBx:diffrn_scale_group code="A24"> <PDBx:I_net>1.021</PDBx:I_net> </PDBx:diffrn_scale_group> </PDBx:diffrn_scale_groupCategory> 0 1 1 diffrn_scale_groupCategory This property indicates that datablock has a category holder diffrn_scale_groupCategory. diffrn_scale_groupCategory This property indicates that diffrn_scale_groupCategory. has a category diffrn_scale_group. diffrn_scale_groupItem Abstract Datatype property for diffrn_scale_group items. reference_to_diffrn_scale_group cross-reference to diffrn_scale_group referenced_by_diffrn_scale_group cross-reference from diffrn_scale_group diffrn_scale_group.I_net The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale. diffrn_scale_group.code The value of attribute code in category diffrn_scale_group must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. 1 2 c1 c2 0 diffrn_source Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_sourceCategory> <PDBx:diffrn_source diffrn_id="s1"> <PDBx:current>180</PDBx:current> <PDBx:power>50</PDBx:power> <PDBx:size>8mm x 0.4 mm broad-focus</PDBx:size> <PDBx:source>rotating anode</PDBx:source> <PDBx:type>Rigaku RU-200</PDBx:type> </PDBx:diffrn_source> </PDBx:diffrn_sourceCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_sourceCategory This property indicates that datablock has a category holder diffrn_sourceCategory. diffrn_sourceCategory This property indicates that diffrn_sourceCategory. has a category diffrn_source. diffrn_sourceItem Abstract Datatype property for diffrn_source items. reference_to_diffrn_source cross-reference to diffrn_source referenced_by_diffrn_source cross-reference from diffrn_source diffrn_source.current The current in milliamperes at which the radiation source was operated. diffrn_source.details A description of special aspects of the radiation source used. diffrn_source.pdbx_synchrotron_beamline Synchrotron beamline. diffrn_source.pdbx_synchrotron_site Synchrotron site. diffrn_source.pdbx_wavelength Wavelength of radiation. diffrn_source.pdbx_wavelength_list Comma separated list of wavelengths or wavelength range. diffrn_source.power The power in kilowatts at which the radiation source was operated. diffrn_source.size The dimensions of the source as viewed from the sample. 8mm x 0.4 mm fine-focus broad focus diffrn_source.source The general class of the radiation source. sealed X-ray tube nuclear reactor spallation source electron microscope rotating-anode X-ray tube synchrotron diffrn_source.take-off_angle The complement of the angle in degrees between the normal to the surface of the X-ray tube target and the primary X-ray beam for beams generated by traditional X-ray tubes. 1.5 H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources. diffrn_source.type The make, model or name of the source of radiation. NSLS beamline X8C Rigaku RU200 diffrn_source.voltage The voltage in kilovolts at which the radiation source was operated. diffrn_source.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_standard_refln Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_standard_reflnCategory> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>2</PDBx:index_k> <PDBx:index_l>4</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>1</PDBx:index_h> <PDBx:index_k>9</PDBx:index_k> <PDBx:index_l>1</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>10</PDBx:index_l> </PDBx:diffrn_standard_refln> </PDBx:diffrn_standard_reflnCategory> 1 1 1 1 1 1 1 1 diffrn_standard_reflnCategory This property indicates that datablock has a category holder diffrn_standard_reflnCategory. diffrn_standard_reflnCategory This property indicates that diffrn_standard_reflnCategory. has a category diffrn_standard_refln. diffrn_standard_reflnItem Abstract Datatype property for diffrn_standard_refln items. reference_to_diffrn_standard_refln cross-reference to diffrn_standard_refln referenced_by_diffrn_standard_refln cross-reference from diffrn_standard_refln diffrn_standard_refln.index_h Miller index h of a standard reflection used in the diffraction measurement process. diffrn_standard_refln.index_k Miller index k of a standard reflection used in the diffraction measurement process. diffrn_standard_refln.index_l Miller index l of a standard reflection used in the diffraction measurement process. diffrn_standard_refln.code The code identifying a reflection measured as a standard reflection with the indices attribute index_h, in category diffrn_standard_refln attribute index_k in category diffrn_standard_refln and attribute index_l in category diffrn_standard_refln. This is the same code as the attribute standard_code in category diffrn_refln in the DIFFRN_REFLN list. 1 2 c1 c2 diffrn_standard_refln.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 diffrn_standards Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_standardsCategory> <PDBx:diffrn_standards diffrn_id="s1"> <PDBx:decay_>0</PDBx:decay_> <PDBx:interval_time>120</PDBx:interval_time> <PDBx:number>3</PDBx:number> </PDBx:diffrn_standards> </PDBx:diffrn_standardsCategory> 0 1 0 1 0 1 0 1 0 1 0 1 1 diffrn_standardsCategory This property indicates that datablock has a category holder diffrn_standardsCategory. diffrn_standardsCategory This property indicates that diffrn_standardsCategory. has a category diffrn_standards. diffrn_standardsItem Abstract Datatype property for diffrn_standards items. reference_to_diffrn_standards cross-reference to diffrn_standards referenced_by_diffrn_standards cross-reference from diffrn_standards diffrn_standards.decay_ The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. diffrn_standards.interval_count The number of reflection intensities between the measurement of standard reflection intensities. diffrn_standards.interval_time The time in minutes between the measurement of standard reflection intensities. diffrn_standards.number The number of unique standard reflections used during the measurement of the diffraction intensities. diffrn_standards.scale_sigma The standard uncertainty (estimated standard deviation) of the individual mean standard scales applied to the intensity data. diffrn_standards.scale_u The standard uncertainty of the individual mean standard scales applied to the intensity data. diffrn_standards.diffrn_id This data item is a pointer to attribute id in category diffrn in the DIFFRN category. 0 em_2d_crystal_entity Data items in the EM_2D_CRYSTAL_ENTITY category record the symmetry details of a 2D crystal assembly component. 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_2d_crystal_entityCategory This property indicates that datablock has a category holder em_2d_crystal_entityCategory. em_2d_crystal_entityCategory This property indicates that em_2d_crystal_entityCategory. has a category em_2d_crystal_entity. em_2d_crystal_entityItem Abstract Datatype property for em_2d_crystal_entity items. reference_to_em_2d_crystal_entity cross-reference to em_2d_crystal_entity referenced_by_em_2d_crystal_entity cross-reference from em_2d_crystal_entity em_2d_crystal_entity.angle_alpha Unit-cell angle alpha of the reported structure, in degrees. em_2d_crystal_entity.angle_beta Unit-cell angle beta of the reported structure, in degrees. em_2d_crystal_entity.angle_gamma Unit-cell angle gamma of the reported structure, in degrees. em_2d_crystal_entity.details Any other details This is a 2-D crystal. em_2d_crystal_entity.length_a Unit-cell length a corresponding to the structure reported, in Angstroms. em_2d_crystal_entity.length_b Unit-cell length b corresponding to the structure reported, in Angstroms. em_2d_crystal_entity.length_c Unit-cell length a corresponding to the structure reported, in Angstroms. P 1 P 2 1 P 1 2 P 1 21 C 1 2 P 2 2 2 P 2 2 21 P 2 21 21 C 2 2 2 P 4 P 4 2 2 P 4 21 2 P 3 P 3 1 2 P 3 2 1 P 6 P 6 2 2 The 17 plane groups are classified as oblique, rectangular, square, and hexagonal. To describe the symmetry of 2D crystals of biological molecules, the plane groups are expanded to their equivalent noncentrosymmetric space groups. The 2D crystal plane corresponds to the 'ab' plane of the space group. . Enumerated space group descriptions include the plane group number in parentheses, the H-M plane group symbol, and the plane group class. em_2d_crystal_entity.entity_assembly_id The value of attribute entity_assembly_id in category em_2d_crystal_entity identifies an assembly component with 2d crystal symmetry. This data item is a pointer to attribute id in category em_entity_assembly in the EM_ENTITY_ASSEMBLY category. em_2d_crystal_entity.id The value of attribute id in category em_2d_crystal_entity must uniquely identify a set of the crystal parameters for this assembly component. 0 em_2d_crystal_grow Data items in the EM_2D_CRYSTAL_GROW category record details of growth conditions for 2d crystal samples. Example 1 - based on PDB entry 1AT9 and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_2d_crystal_growCategory> <PDBx:em_2d_crystal_grow id="1"> <PDBx:apparatus xsi:nil="true" /> <PDBx:atmosphere>room air</PDBx:atmosphere> <PDBx:buffer_id>2</PDBx:buffer_id> <PDBx:citation_id>2</PDBx:citation_id> <PDBx:details>on grid</PDBx:details> <PDBx:mean_2d_crystal_size xsi:nil="true" /> <PDBx:method xsi:nil="true" /> <PDBx:number_2d_crystals>129</PDBx:number_2d_crystals> <PDBx:pH>5.2</PDBx:pH> <PDBx:temp>18</PDBx:temp> <PDBx:time xsi:nil="true" /> </PDBx:em_2d_crystal_grow> </PDBx:em_2d_crystal_growCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 em_2d_crystal_growCategory This property indicates that datablock has a category holder em_2d_crystal_growCategory. em_2d_crystal_growCategory This property indicates that em_2d_crystal_growCategory. has a category em_2d_crystal_grow. em_2d_crystal_growItem Abstract Datatype property for em_2d_crystal_grow items. reference_to_em_2d_crystal_grow cross-reference to em_2d_crystal_grow referenced_by_em_2d_crystal_grow cross-reference from em_2d_crystal_grow em_2d_crystal_grow.apparatus The type of the apparatus used for growing the crystals. Langmuir trough em_2d_crystal_grow.atmosphere The type of atmosphere in which crystals were grown. room air em_2d_crystal_grow.buffer_id This data item is a pointer to attribute id in category em_buffer in the BUFFER category. em_2d_crystal_grow.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_2d_crystal_grow.details Any additional items concerning 2d crystal growth. em_2d_crystal_grow.mean_2d_crystal_size The approximate size (microns squared) of 2d crystals imaged. em_2d_crystal_grow.method The method used for growing the crystals. lipid monolayer em_2d_crystal_grow.number_2d_crystals The number of 2d crystals imaged. em_2d_crystal_grow.pH the pH value used for growing the crystals. 4.7 em_2d_crystal_grow.temp The value of the temperature in degrees Kelvin used for growing the crystals. 293 em_2d_crystal_grow.time The length of time required to grow the crystals. approximately 2 days em_2d_crystal_grow.id The value of attribute crystal_id in category em_2d_crystal_grow must uniquely identify the sample 2d crystal. 0 em_2d_projection_selection Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_2d_projection_selectionCategory> <PDBx:em_2d_projection_selection entry_id="1"> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_particles>5267</PDBx:num_particles> <PDBx:software_name>1</PDBx:software_name> </PDBx:em_2d_projection_selection> </PDBx:em_2d_projection_selectionCategory> 0 1 0 1 0 1 0 1 0 1 1 em_2d_projection_selectionCategory This property indicates that datablock has a category holder em_2d_projection_selectionCategory. em_2d_projection_selectionCategory This property indicates that em_2d_projection_selectionCategory. has a category em_2d_projection_selection. em_2d_projection_selectionItem Abstract Datatype property for em_2d_projection_selection items. reference_to_em_2d_projection_selection cross-reference to em_2d_projection_selection referenced_by_em_2d_projection_selection cross-reference from em_2d_projection_selection em_2d_projection_selection.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_2d_projection_selection.details Any additional details used for selecting observed assemblies. negative monitor contrast facilitated particle picking em_2d_projection_selection.method The method used for selecting observed assemblies. particles picked interactively from monitor em_2d_projection_selection.num_particles The number of particles selected from the projection set of images. 840 em_2d_projection_selection.software_name This data item is a pointer to attribute name in category software in the SOFTWARE category. em_2d_projection_selection.entry_id The value of attribute entry_id in category em_2d_projection_selection points to the ENTRY category. 0 em_3d_fitting Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fittingCategory> <PDBx:em_3d_fitting entry_id="1DYL" id="1"> <PDBx:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. </PDBx:details> <PDBx:method>AUTOMATIC</PDBx:method> <PDBx:overall_b_value xsi:nil="true" /> <PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol> <PDBx:ref_space>REAL</PDBx:ref_space> <PDBx:software_name>1</PDBx:software_name> <PDBx:target_criteria>R-FACTOR</PDBx:target_criteria> </PDBx:em_3d_fitting> </PDBx:em_3d_fittingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_3d_fittingCategory This property indicates that datablock has a category holder em_3d_fittingCategory. em_3d_fittingCategory This property indicates that em_3d_fittingCategory. has a category em_3d_fitting. em_3d_fittingItem Abstract Datatype property for em_3d_fitting items. reference_to_em_3d_fitting cross-reference to em_3d_fitting referenced_by_em_3d_fitting cross-reference from em_3d_fitting em_3d_fitting.details Any additional details regarding fitting of atomic coordinates into the 3d-em volume. Initial local fitting was done using Chimera and then NMFF was used for flexible fitting. em_3d_fitting.method The method used to fit atomic coordinates into the 3dem reconstructed map. Local refinement, Flexible fitting em_3d_fitting.overall_b_value The overall B (temperature factor) value for the 3d-em volume. 200 em_3d_fitting.ref_protocol The type of protocol used in the refinement. rigid body REAL RECIPROCAL A flag to indicate whether fitting was carried out in real or reciprocal refinement space. Real Reciprocal em_3d_fitting.software_name The software used for fitting atomic coordinates to the map. Situs, NMFF, YUP.scx, etc. em_3d_fitting.target_criteria The quality of fit of the atomic coordinates into the 3dem volume map. Cross-correlation coefficient em_3d_fitting.entry_id This data item is a pointer to _entry_id in the ENTRY category. em_3d_fitting.id The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. 0 em_3d_fitting_list Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fitting_listCategory> <PDBx:em_3d_fitting_list _3d_fitting_id="l" id="1"> <PDBx:pdb_chain_id xsi:nil="true" /> <PDBx:pdb_entry_id>1VCQ</PDBx:pdb_entry_id> </PDBx:em_3d_fitting_list> </PDBx:em_3d_fitting_listCategory> 0 1 0 1 1 1 em_3d_fitting_listCategory This property indicates that datablock has a category holder em_3d_fitting_listCategory. em_3d_fitting_listCategory This property indicates that em_3d_fitting_listCategory. has a category em_3d_fitting_list. em_3d_fitting_listItem Abstract Datatype property for em_3d_fitting_list items. reference_to_em_3d_fitting_list cross-reference to em_3d_fitting_list referenced_by_em_3d_fitting_list cross-reference from em_3d_fitting_list em_3d_fitting_list.pdb_chain_id The chain id for the entry used in fitting. em_3d_fitting_list.pdb_entry_id The PDB code for the entry used in fitting. PDB entry 1EHZ em_3d_fitting_list._3d_fitting_id The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer to attribute id in category em_3d_fitting in the 3d_fitting category em_3d_fitting_list.id This data item is a unique identifier. 0 em_3d_reconstruction Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_reconstructionCategory> <PDBx:em_3d_reconstruction entry_id="1DYL" id="1"> <PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:ctf_correction_method xsi:nil="true" /> <PDBx:details xsi:nil="true" /> <PDBx:method>CROSS-COMMON LINES</PDBx:method> <PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size> <PDBx:resolution>9</PDBx:resolution> <PDBx:resolution_method xsi:nil="true" /> </PDBx:em_3d_reconstruction> </PDBx:em_3d_reconstructionCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_3d_reconstructionCategory This property indicates that datablock has a category holder em_3d_reconstructionCategory. em_3d_reconstructionCategory This property indicates that em_3d_reconstructionCategory. has a category em_3d_reconstruction. em_3d_reconstructionItem Abstract Datatype property for em_3d_reconstruction items. reference_to_em_3d_reconstruction cross-reference to em_3d_reconstruction referenced_by_em_3d_reconstruction cross-reference from em_3d_reconstruction em_3d_reconstruction.actual_pixel_size The actual pixel size of projection set of images. 2.8 5.76 em_3d_reconstruction.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_3d_reconstruction.ctf_correction_method The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. The volumes were CTF-corrected in defocus groups, with an average of approximately 999 individual images per group em_3d_reconstruction.details Any additional details used in the 3d reconstruction. a modified version of SPIDER program was used for the reconstruction em_3d_reconstruction.euler_angles_details euler angles details em_3d_reconstruction.magnification_calibration The magnification calibration method for the 3d reconstruction. TMV images em_3d_reconstruction.method The algorithm method used for the 3d-reconstruction. cross-common lines polar Fourier transform (PFT) em_3d_reconstruction.nominal_pixel_size The nominal pixel size of the projection set of images. 3.11 6.78 em_3d_reconstruction.num_class_averages This item was correspondence to two type of em dataset processing_emDataSet_singleParticle.numClassAverages processing_emDataSet_icosahedral.numClassAverages em_3d_reconstruction.num_particles The number of particles used in the 3d reconstruction em_3d_reconstruction.resolution The final resolution (in angstroms)of the 3d reconstruction. 8.9 10.0 em_3d_reconstruction.resolution_method The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off em_3d_reconstruction.software software name em_3d_reconstruction.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_3d_reconstruction.id The value of attribute id in category em_3d_reconstruction must uniquely identify the 3d reconstruction. 0 em_assembly Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_assemblyCategory> <PDBx:em_assembly entry_id="1DYL" id="1"> <PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state> <PDBx:composition>virus</PDBx:composition> <PDBx:details xsi:nil="true" /> <PDBx:mol_wt_exp xsi:nil="true" /> <PDBx:mol_wt_method xsi:nil="true" /> <PDBx:mol_wt_theo xsi:nil="true" /> <PDBx:name>virus</PDBx:name> <PDBx:num_components>1</PDBx:num_components> </PDBx:em_assembly> </PDBx:em_assemblyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_assemblyCategory This property indicates that datablock has a category holder em_assemblyCategory. em_assemblyCategory This property indicates that em_assemblyCategory. has a category em_assembly. em_assemblyItem Abstract Datatype property for em_assembly items. reference_to_em_assembly cross-reference to em_assembly referenced_by_em_assembly cross-reference from em_assembly 2D CRYSTAL 3D CRYSTAL INDIVIDUAL STRUCTURE FILAMENT ICOSAHEDRAL PARTICLE TISSUE CELL A description of the aggregation state of the assembly. 2D CRYSTAL 3D CRYSTAL FILAMENT PARTICLE TISSUE CELL em_assembly.composition The known composition of the assembly. em_assembly.details A description of any additional details describing the observed sample. This sample was monodisperse. em_assembly.mol_wt_exp The value (in megadaltons) of the experimentally determined molecular weight of the assembly. em_assembly.mol_wt_method The method used in determining the molecular weight. em_assembly.mol_wt_theo The value (in megadaltons) of the theoretically determined molecular weight of the assembly. em_assembly.name The name of the assembly of observed complexes. Fab Fragment of Mab1-Ia monoclonal antibody bound to Human Rhinovirus1h Nim-Ia Site em_assembly.num_components The number of components of the biological assembly. em_assembly.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_assembly.id The value of attribute id in category em_assembly must uniquely identify a collection of observed complexes. 0 em_buffer Data items in the BUFFER category record details of the sample buffer. 0 1 0 1 1 em_bufferCategory This property indicates that datablock has a category holder em_bufferCategory. em_bufferCategory This property indicates that em_bufferCategory. has a category em_buffer. em_bufferItem Abstract Datatype property for em_buffer items. reference_to_em_buffer cross-reference to em_buffer referenced_by_em_buffer cross-reference from em_buffer em_buffer.details Additional details about the buffer. 20mM NaCl, 10mM Tris-HCL,1mM MgCl2,1mM em_buffer.name The name of the buffer. Polymix buffer em_buffer.id The value of attribute id in category em_buffer must uniquely identify the sample buffer. 0 em_buffer_components Constituents of buffer in sample Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_buffer_componentsCategory> <PDBx:em_buffer_components buffer_id="1" id="1"> <PDBx:conc>4 </PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>NaCl</PDBx:name> <PDBx:volume>0.200 </PDBx:volume> </PDBx:em_buffer_components> <PDBx:em_buffer_components buffer_id="1" id="2"> <PDBx:conc>100</PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:volume>0.047 </PDBx:volume> </PDBx:em_buffer_components> <PDBx:em_buffer_components buffer_id="1" id="3"> <PDBx:conc>neat</PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>water</PDBx:name> <PDBx:volume>0.700 </PDBx:volume> </PDBx:em_buffer_components> </PDBx:em_buffer_componentsCategory> 0 1 0 1 0 1 0 1 1 1 em_buffer_componentsCategory This property indicates that datablock has a category holder em_buffer_componentsCategory. em_buffer_componentsCategory This property indicates that em_buffer_componentsCategory. has a category em_buffer_components. em_buffer_componentsItem Abstract Datatype property for em_buffer_components items. reference_to_em_buffer_components cross-reference to em_buffer_components referenced_by_em_buffer_components cross-reference from em_buffer_components em_buffer_components.conc The millimolar concentration of buffer component. 200 em_buffer_components.details Any additional details to do with buffer composition. pH adjusted with NaOH em_buffer_components.name The name of each buffer component. Acetic acid em_buffer_components.volume The volume of buffer component. 0.200 em_buffer_components.buffer_id This data item is a pointer to attribute id in category em_buffer in the BUFFER category. em_buffer_components.id The value of attribute id in category em_buffer_components must uniquely identify a component of the buffer. 0 em_detector Data items in the EM_DETECTOR category record details of the image detector type. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_detectorCategory> <PDBx:em_detector entry_id="1DYL" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:detective_quantum_efficiency xsi:nil="true" /> <PDBx:type>KODAK SO163 FILM</PDBx:type> </PDBx:em_detector> </PDBx:em_detectorCategory> 0 1 0 1 0 1 1 1 em_detectorCategory This property indicates that datablock has a category holder em_detectorCategory. em_detectorCategory This property indicates that em_detectorCategory. has a category em_detector. em_detectorItem Abstract Datatype property for em_detector items. reference_to_em_detector cross-reference to em_detector referenced_by_em_detector cross-reference from em_detector em_detector.details Any additional information about the detection system. Any other details regarding the detector. em_detector.detective_quantum_efficiency The detective_quantum_efficiency (DQE)is defined as the square of the signal-to-noise ratio in the recording device divided by the square of the signal-to-ratio in the electron beam: (SIGNAL/NOISE)2 recording device DQE = ------------------------------- (SIGNAL/NOISE)2 electron beam A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas that the signal-to-noise ratio is reduced by half in the recording step. (0.5)**2 DQE = --------- = 0.25. (1.0)**2 0.25 em_detector.type The detector type used for recording images. Usually film or CCD camera. KODAK SO163 FILM GATAN 673 GATAN 676 GATAN 692 GATAN 794 GATAN 1000 GATAN 4000 TVIPS BIOCAM TVIPS TEMCAM F214 TVIPS TEMCAM F224 TVIPS FASTSCAN F114 PROSCAN AMT em_detector.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_detector.id The value of attribute id in category em_detector must uniquely identify the detector used for imaging. 0 em_electron_diffraction Data items in the EM_ELECTRON_DIFFRACTION category record details about the electron diffraction data from the electron crystallography experiment. Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB <PDBx:em_electron_diffractionCategory> <PDBx:em_electron_diffraction entry_id="1TUB" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:num_diff_patterns xsi:nil="true" /> <PDBx:num_structure_factors>12000</PDBx:num_structure_factors> </PDBx:em_electron_diffraction> </PDBx:em_electron_diffractionCategory> 1 1 0 1 0 1 1 1 em_electron_diffractionCategory This property indicates that datablock has a category holder em_electron_diffractionCategory. em_electron_diffractionCategory This property indicates that em_electron_diffractionCategory. has a category em_electron_diffraction. em_electron_diffractionItem Abstract Datatype property for em_electron_diffraction items. reference_to_em_electron_diffraction cross-reference to em_electron_diffraction referenced_by_em_electron_diffraction cross-reference from em_electron_diffraction em_electron_diffraction.details Details of the electron diffraction experiment THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. 1 em_electron_diffraction.num_diff_patterns The number of diffraction patterns used from the electron diffraction experiment. em_electron_diffraction.num_structure_factors The number of structure factors from the electron diffraction experiment. 12000 em_electron_diffraction.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_electron_diffraction.id The value of attribute id in category electron_diffraction must uniquely identify the electron diffraction experiment. 0 em_electron_diffraction_pattern data items in the em_electron_diffraction_pattern category record details about the pattern information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <PDBx:em_electron_diffraction_patternCategory> <PDBx:em_electron_diffraction_pattern entry_id="1TUB" id="1"> <PDBx:num_images_by_tilt_angle>4</PDBx:num_images_by_tilt_angle> <PDBx:num_patterns_by_tilt_angle>1</PDBx:num_patterns_by_tilt_angle> <PDBx:tilt_angle xsi:nil="true" /> </PDBx:em_electron_diffraction_pattern> </PDBx:em_electron_diffraction_patternCategory> 0 1 0 1 0 1 1 1 em_electron_diffraction_patternCategory This property indicates that datablock has a category holder em_electron_diffraction_patternCategory. em_electron_diffraction_patternCategory This property indicates that em_electron_diffraction_patternCategory. has a category em_electron_diffraction_pattern. em_electron_diffraction_patternItem Abstract Datatype property for em_electron_diffraction_pattern items. reference_to_em_electron_diffraction_pattern cross-reference to em_electron_diffraction_pattern referenced_by_em_electron_diffraction_pattern cross-reference from em_electron_diffraction_pattern em_electron_diffraction_pattern.num_images_by_tilt_angle the number of images by tilt angle. 4 em_electron_diffraction_pattern.num_patterns_by_tilt_angle the number of diffraction patterns by tilt angle. 1 em_electron_diffraction_pattern.tilt_angle the tilt angle at which the diffraction pattern was obtained. em_electron_diffraction_pattern.entry_id this data item is a pointer to attribute id in category entry in the entry category. em_electron_diffraction_pattern.id the value of attribute id in category electron_diffraction_pattern must uniquely identify the electron diffraction pattern experiment. 0 em_electron_diffraction_phase data items in the em_electron_diffraction_phase category record details about the phase information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <PDBx:em_electron_diffraction_phaseCategory> <PDBx:em_electron_diffraction_phase entry_id="1TUB" id="1"> <PDBx:d_res_high>4</PDBx:d_res_high> <PDBx:highest_resolution_shell_error xsi:nil="true" /> <PDBx:overall_error xsi:nil="true" /> <PDBx:rejection_criteria_error xsi:nil="true" /> <PDBx:residual xsi:nil="true" /> </PDBx:em_electron_diffraction_phase> </PDBx:em_electron_diffraction_phaseCategory> 0 1 0 1 0 1 0 1 0 1 1 1 em_electron_diffraction_phaseCategory This property indicates that datablock has a category holder em_electron_diffraction_phaseCategory. em_electron_diffraction_phaseCategory This property indicates that em_electron_diffraction_phaseCategory. has a category em_electron_diffraction_phase. em_electron_diffraction_phaseItem Abstract Datatype property for em_electron_diffraction_phase items. reference_to_em_electron_diffraction_phase cross-reference to em_electron_diffraction_phase referenced_by_em_electron_diffraction_phase cross-reference from em_electron_diffraction_phase em_electron_diffraction_phase.d_res_high the highest resolution d-value for the electron diffraction experiment. 5 em_electron_diffraction_phase.highest_resolution_shell_error the highest resolution shell error in degrees. em_electron_diffraction_phase.overall_error the overall phase error in degrees. em_electron_diffraction_phase.rejection_criteria_error the rejection criteria (phase error) in degrees. em_electron_diffraction_phase.residual the phase residual value for the electron diffraction experiment. em_electron_diffraction_phase.entry_id this data item is a pointer to attribute id in category entry in the entry category. em_electron_diffraction_phase.id the value of attribute id in category electron_diffraction_phase must uniquely identify the electron diffraction phase experiment. 0 em_entity_assembly Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_entity_assemblyCategory> <PDBx:em_entity_assembly assembly_id="1" id="1"> <PDBx:type>VIRUS</PDBx:type> </PDBx:em_entity_assembly> </PDBx:em_entity_assemblyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_entity_assemblyCategory This property indicates that datablock has a category holder em_entity_assemblyCategory. em_entity_assemblyCategory This property indicates that em_entity_assemblyCategory. has a category em_entity_assembly. em_entity_assemblyItem Abstract Datatype property for em_entity_assembly items. reference_to_em_entity_assembly cross-reference to em_entity_assembly referenced_by_em_entity_assembly cross-reference from em_entity_assembly em_entity_assembly.details Additional details about the component. Fab fragment generated by proteolytic cleavage of LA2 IgG antibody. em_entity_assembly.ebi_cell The cell from which the component was obtained. CHO HELA 3T3 em_entity_assembly.ebi_cellular_location The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane YES NO A flag to indicate whether the component is engineered. em_entity_assembly.ebi_expression_system The expression system used to produce the component. eschericia coli saccharomyces cerevisiae em_entity_assembly.ebi_expression_system_plasmid The plasmid used in the expression system used to produce the component. pBR322 pMB9 em_entity_assembly.ebi_organelle The organelle from which the component was obtained. golgi mitochondrion cytoskeleton em_entity_assembly.ebi_organism_common The common name of the species of the natural organism from which the component was obtained. em_entity_assembly.ebi_organism_scientific The species of the natural organism from which the component was obtained. em_entity_assembly.ebi_strain The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 em_entity_assembly.ebi_tissue The tissue of the natural organism from which the component was obtained. heart liver eye lens em_entity_assembly.go_id The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). GO:0005876 GO:0015630 em_entity_assembly.ipr_id The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). 001304 002353 YES NO mutant flag em_entity_assembly.name The name of the component of the observed assembly. messenger RNA initiation factor 2 GroEL antibody Fab fragment em_entity_assembly.number_of_copies number of copies em_entity_assembly.oligomeric_details oligomeric details em_entity_assembly.synonym Alternative name of the component. FADV-1 VIRUS PROTEIN NUCLEIC ACID LIGAND LABEL CELLULAR COMPONENT RIBOSOME A description of types of components of the assembly of the biological structure. em_entity_assembly.assembly_id This data item is a pointer to attribute id in category em_assembly in the ASSEMBLY category. em_entity_assembly.id The value of attribute id in category em_entity_assembly must uniquely identify each of the components of the complex. 0 em_entity_assembly_list Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each component. Example 1 - microtubule <PDBx:em_entity_assembly_listCategory> <PDBx:em_entity_assembly_list entity_assembly_id="1" entity_id="1" id="1"> <PDBx:number_of_copies>2</PDBx:number_of_copies> <PDBx:oligomeric_details>DIMER</PDBx:oligomeric_details> </PDBx:em_entity_assembly_list> </PDBx:em_entity_assembly_listCategory> 0 1 0 1 1 1 1 em_entity_assembly_listCategory This property indicates that datablock has a category holder em_entity_assembly_listCategory. em_entity_assembly_listCategory This property indicates that em_entity_assembly_listCategory. has a category em_entity_assembly_list. em_entity_assembly_listItem Abstract Datatype property for em_entity_assembly_list items. reference_to_em_entity_assembly_list cross-reference to em_entity_assembly_list referenced_by_em_entity_assembly_list cross-reference from em_entity_assembly_list em_entity_assembly_list.number_of_copies The number of copies of the entity. em_entity_assembly_list.oligomeric_details The oligomeric state of the entity. em_entity_assembly_list.entity_assembly_id This data item is a pointer to attribute id in category em_entity_assembly in the ENTITY_ASSEMBLY category. em_entity_assembly_list.entity_id A pointer to entity id. em_entity_assembly_list.id The value of attribute id in category em_entity_assembly_list must uniquely identify the component. 0 em_euler_angle_distribution Data items in the EM_EULER_ANGLE_DISTRIBUTION category record details of assignment of Euler angles for projection sets of particles. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_euler_angle_distributionCategory> <PDBx:em_euler_angle_distribution entry_id="1DYL" id="1"> <PDBx:alpha xsi:nil="true" /> <PDBx:beta xsi:nil="true" /> <PDBx:details xsi:nil="true" /> <PDBx:gamma xsi:nil="true" /> </PDBx:em_euler_angle_distribution> </PDBx:em_euler_angle_distributionCategory> 0 1 0 1 0 1 0 1 1 1 em_euler_angle_distributionCategory This property indicates that datablock has a category holder em_euler_angle_distributionCategory. em_euler_angle_distributionCategory This property indicates that em_euler_angle_distributionCategory. has a category em_euler_angle_distribution. em_euler_angle_distributionItem Abstract Datatype property for em_euler_angle_distribution items. reference_to_em_euler_angle_distribution cross-reference to em_euler_angle_distribution referenced_by_em_euler_angle_distribution cross-reference from em_euler_angle_distribution em_euler_angle_distribution.alpha The euler-alpha angle assignment. 90 em_euler_angle_distribution.beta The euler-beta angle assignment. 90 em_euler_angle_distribution.details Any additional details of the euler angles distribution and assignment. em_euler_angle_distribution.gamma The euler-gamma angle assignment. 0 em_euler_angle_distribution.entry_id The value of attribute entry_id in category em_euler_angle_distribution is a pointer to the ENTRY category. em_euler_angle_distribution.id The value of attribute id in category em_euler_angle_distribution must uniquely identify the euler angle assignments of the projection set used in the final reconstruction. 0 em_experiment Data items in the EM_EXPERIMENT category provide high-level classification of the EM experiment. Example 1 - based on PDB entry 1EG0 <PDBx:em_experimentCategory> <PDBx:em_experiment entry_id="1EG0"> <PDBx:reconstruction_method>SINGLE PARTICLE</PDBx:reconstruction_method> <PDBx:specimen_type>VITREOUS ICE (CRYO EM)</PDBx:specimen_type> </PDBx:em_experiment> </PDBx:em_experimentCategory> 0 1 0 1 1 em_experimentCategory This property indicates that datablock has a category holder em_experimentCategory. em_experimentCategory This property indicates that em_experimentCategory. has a category em_experiment. em_experimentItem Abstract Datatype property for em_experiment items. reference_to_em_experiment cross-reference to em_experiment referenced_by_em_experiment cross-reference from em_experiment SINGLE PARTICLE HELICAL CRYSTALLOGRAPHY TOMOGRAPHY The reconstruction method used in the EM experiment. em_experiment.specimen_type The specimen type used in the EM experiment. VITREOUS ICE (CRYO EM) NEGATIVE STAIN FREEZE SUBSTITUTION em_experiment.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 em_helical_entity 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_helical_entityCategory This property indicates that datablock has a category holder em_helical_entityCategory. em_helical_entityCategory This property indicates that em_helical_entityCategory. has a category em_helical_entity. em_helical_entityItem Abstract Datatype property for em_helical_entity items. reference_to_em_helical_entity cross-reference to em_helical_entity referenced_by_em_helical_entity cross-reference from em_helical_entity em_helical_entity.angular_rotation_per_subunit The angular rotation per helical subunit in degrees. -34.616000 em_helical_entity.axial_rise_per_subunit The axial rise per subunit in the helical assembly. 17.400000 em_helical_entity.axial_symmetry n-fold symmetry along the filament helix axis. 1 5 7 em_helical_entity.details Any other details regarding the helical assembly Dihedral symmetry YES NO Value should be YES if a the filament has two-fold symmetry perpendicular to the helical axis. em_helical_entity.hand Handedness of the helix: right handed or left handed Right Left em_helical_entity.entity_assembly_id The value of attribute entity_assembly_id in category em_helical_entity identifies a particular assembly component. This data item is a pointer to attribute id in category entity_assembly in the EM_ENTITY_ASSEMBLY category. em_helical_entity.id The value of attribute id in category em_helical_entity must uniquely identify a set of the filament parameters for this assembly component. 0 em_icos_virus_shells Data items in the EM_ICOS_VIRUS_SHELLS category record details of the viral shell number, diameter of each shell and triangulation number. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_icos_virus_shellsCategory> <PDBx:em_icos_virus_shells id="1" virus_entity_id="1"> <PDBx:shell_diameter>400</PDBx:shell_diameter> <PDBx:triangulation_num>4</PDBx:triangulation_num> </PDBx:em_icos_virus_shells> </PDBx:em_icos_virus_shellsCategory> 0 1 0 1 1 1 em_icos_virus_shellsCategory This property indicates that datablock has a category holder em_icos_virus_shellsCategory. em_icos_virus_shellsCategory This property indicates that em_icos_virus_shellsCategory. has a category em_icos_virus_shells. em_icos_virus_shellsItem Abstract Datatype property for em_icos_virus_shells items. reference_to_em_icos_virus_shells cross-reference to em_icos_virus_shells referenced_by_em_icos_virus_shells cross-reference from em_icos_virus_shells em_icos_virus_shells.shell_diameter The value of the diameter (in angstroms) for each protein shell of the virus. em_icos_virus_shells.triangulation_num The triangulation number (T number) is a geometric and abstract concept that does not correspond to the structural components of an individul virus. It refers to the organisation of the geometric figure. The triangulation number, T is given by the following relationship: T= h*2 + hk +k*2, where h and k are positive integers which define the position of the five-fold vertex on the original hexagonal net. 4 em_icos_virus_shells.id The value of attribute id in category em_em_icos_virus_shells must uniquely identify the number and diameter of each virus protein shell and its triangulation number. em_icos_virus_shells.virus_entity_id The value of attribute virus_entity_id in category em_icos_virus_shells is a pointer to attribute id in category em_virus_entity in the VIRUS_ENTITY category. 0 em_image_scans Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_image_scansCategory> <PDBx:em_image_scans entry_id="1DYL" id="2"> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:details xsi:nil="true" /> <PDBx:number_digital_images>48</PDBx:number_digital_images> <PDBx:od_range xsi:nil="true" /> <PDBx:quant_bit_size xsi:nil="true" /> <PDBx:sampling_size xsi:nil="true" /> <PDBx:scanner_model xsi:nil="true" /> </PDBx:em_image_scans> </PDBx:em_image_scansCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_image_scansCategory This property indicates that datablock has a category holder em_image_scansCategory. em_image_scansCategory This property indicates that em_image_scansCategory. has a category em_image_scans. em_image_scansItem Abstract Datatype property for em_image_scans items. reference_to_em_image_scans cross-reference to em_image_scans referenced_by_em_image_scans cross-reference from em_image_scans em_image_scans.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_image_scans.details Any additional details about scanning images. em_image_scans.number_digital_images The number of images scanned and digitised. em_image_scans.od_range The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. 1.4 em_image_scans.quant_bit_size The number of bits per pixel. 8 em_image_scans.sampling_size The sampling step size (microns) set on the scanner. ZEISS SCAI EMIL 10 OPTRONICS PERKIN ELMER TEMSCAN EIKONIX IEEE 488 NIKON COOLSCAN NIKON SUPER COOLSCAN 9000 IMAGE SCIENCE PATCHWORK DENSITOMETER PRIMESCAN OTHER The scanner model. em_image_scans.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_image_scans.id The value of attribute id in category em_image_scans must uniquely identify the images scanned. 0 em_imaging Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_imagingCategory> <PDBx:em_imaging entry_id="1DYL" id="1"> <PDBx:accelerating_voltage>200</PDBx:accelerating_voltage> <PDBx:calibrated_magnification xsi:nil="true" /> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:date>1998-15-06</PDBx:date> <PDBx:details xsi:nil="true" /> <PDBx:detector_distance xsi:nil="true" /> <PDBx:electron_dose xsi:nil="true" /> <PDBx:electron_source>FEG</PDBx:electron_source> <PDBx:energy_filter xsi:nil="true" /> <PDBx:energy_window xsi:nil="true" /> <PDBx:illumination_mode>bright field</PDBx:illumination_mode> <PDBx:microscope_model>FEI/PHILIPS CM200 FEG</PDBx:microscope_model> <PDBx:mode>low dose</PDBx:mode> <PDBx:nominal_cs>2.0</PDBx:nominal_cs> <PDBx:nominal_defocus_max>7600</PDBx:nominal_defocus_max> <PDBx:nominal_defocus_min>975</PDBx:nominal_defocus_min> <PDBx:nominal_magnification>50000</PDBx:nominal_magnification> <PDBx:recording_temperature_maximum xsi:nil="true" /> <PDBx:recording_temperature_minimum xsi:nil="true" /> <PDBx:sample_support_id>1</PDBx:sample_support_id> <PDBx:specimen_holder_model>gatan 626-0300</PDBx:specimen_holder_model> <PDBx:specimen_holder_type>cryotransfer</PDBx:specimen_holder_type> <PDBx:temperature>95</PDBx:temperature> <PDBx:tilt_angle_max>0</PDBx:tilt_angle_max> <PDBx:tilt_angle_min>0</PDBx:tilt_angle_min> </PDBx:em_imaging> </PDBx:em_imagingCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 0 1 0 1 0 1 0 1 0 1 1 1 em_imagingCategory This property indicates that datablock has a category holder em_imagingCategory. em_imagingCategory This property indicates that em_imagingCategory. has a category em_imaging. em_imagingItem Abstract Datatype property for em_imaging items. reference_to_em_imaging cross-reference to em_imaging referenced_by_em_imaging cross-reference from em_imaging em_imaging.accelerating_voltage A value of accelerating voltage (in kV) used for imaging. 300 em_imaging.astigmatism astigmatism em_imaging.calibrated_magnification The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. 61200 em_imaging.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_imaging.date Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. 2001-05-08 em_imaging.details Any additional imaging details. weak beam illumination em_imaging.detector_distance The camera length (in millimetres). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. em_imaging.detector_id The value of attribute detector_id in category em_imaging must uniquely identify the type of detector used in the experiment. em_imaging.electron_beam_tilt_params electron beam tilt params em_imaging.electron_dose The electron dose received by the specimen (electrons per square angstrom). 0.9 em_imaging.electron_source The source of electrons. The electron gun. FIELD EMISSION GUN LAB6 TUNGSTEN HAIRPIN SCHOTTKY FIELD EMISSION GUN OTHER em_imaging.energy_filter The type of energy filter spectrometer apparatus. FEI em_imaging.energy_window The energy filter range in electron volts (eV)set by spectrometer. 0 - 15 em_imaging.illumination_mode The mode of illumination. FLOOD BEAM FLOOD BEAM LOW DOSE SPOT SCAN OTHER em_imaging.microscope_id This data item is a pointer to attribute id in category em_microscope in the EM_MICROSCOPE category. em_imaging.microscope_model The name of the model of microscope. HITACHI H8100 HITACHI HF2000 HITACHI HF2000-UHR HITACHI H9000-UHR HITACHI H9000-NAR HITACHI 300KEV FEG HITACHI HU1250 HITACHI H-1500 JEOL 2000EX JEOL 2010HT JEOL 2010UHR JEOL 2010F JEOL 3010HT JEOL 3010UHR JEOL KYOTO-3000SFF JEOL 4000EX JEOL HAREM JEOL ARM-1000 JEOL KYOTO-1000 JEOL ARM-1250 FEI/PHILIPS CM120T FEI/PHILIPS CM200T FEI/PHILIPS CM20/ST FEI/PHILIPS CM20/SOPHIE FEI/PHILIPS CM200FEG/ST FEI/PHILIPS CM20/UT FEI/PHILIPS CM200FEG/UT FEI/PHILIPS CM30/T FEI/PHILIPS CM300FEG/T FEI/PHILIPS CM300FEG/HE FEI/PHILIPS CM30/ST FEI/PHILIPS CM300FEG/ST FEI/PHILIPS CM300FEG/UT FEI TECNAI 12 FEI TECNAI 20 FEI TECNAI F20 FEI TECNAI F30 FEI MORGAGNI em_imaging.mode The mode of imaging. BRIGHT FIELD DARK FIELD DIFFRACTION OTHER em_imaging.nominal_cs The spherical aberration coefficient (Cs) in millimetres, of the objective lens. 1.4 em_imaging.nominal_defocus_max The maximum defocus value of the objective lens (in nanometres) used to obtain the recorded images. 5000 em_imaging.nominal_defocus_min The minimum defocus value of the objective lens (in nanometres) used to obtain the recorded images. 1200 em_imaging.nominal_magnification The magnification indicated by the microscope readout. 60000 em_imaging.recording_temperature_maximum The specimen temperature maximum (degrees Kelvin) for the duration of imaging. em_imaging.recording_temperature_minimum The specimen temperature minimum (degrees Kelvin) for the duration of imaging. em_imaging.sample_support_id This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. em_imaging.scans_id The value of attribute scans_id in category em_imaging must uniquely identify the image_scans used in the experiment. GATAN HELIUM GATAN LIQUID NITROGEN JEM3200FSC CRYOHOLDER PHILIPS ROTATION HOLDER HOME BUILD JEOL SIDE ENTRY, EUCENTRIC OTHER The name of the model of specimen holder used during imaging. em_imaging.specimen_holder_type The type of specimen holder used during imaging. cryo em_imaging.temperature The mean specimen stage temperature (degrees Kelvin) during imaging in the microscope. 70 em_imaging.tilt_angle_max The maximum angle at which the specimen was tilted to obtain recorded images. 70 em_imaging.tilt_angle_min The minimum angle at which the specimen was tilted to obtain recorded images. -70 em_imaging.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_imaging.id The value of attribute id in category em_imaging must uniquely identify each imaging experiment. 0 em_sample_preparation Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to loading onto grid support. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_preparationCategory> <PDBx:em_sample_preparation entry_id="1DYL" id="1"> <PDBx:_2d_crystal_grow_id xsi:nil="true" /> <PDBx:buffer_id>1</PDBx:buffer_id> <PDBx:ph>7.6</PDBx:ph> <PDBx:sample_concentration>5</PDBx:sample_concentration> <PDBx:support_id>1</PDBx:support_id> </PDBx:em_sample_preparation> </PDBx:em_sample_preparationCategory> 0 1 0 1 0 1 1 1 0 1 0 1 0 1 1 1 em_sample_preparationCategory This property indicates that datablock has a category holder em_sample_preparationCategory. em_sample_preparationCategory This property indicates that em_sample_preparationCategory. has a category em_sample_preparation. em_sample_preparationItem Abstract Datatype property for em_sample_preparation items. reference_to_em_sample_preparation cross-reference to em_sample_preparation referenced_by_em_sample_preparation cross-reference from em_sample_preparation em_sample_preparation._2d_crystal_grow_id This data item is a pointer to attribute id in category em_2d_crystal_grow in the 2D_CRYSTAL_GROW category. em_sample_preparation.buffer_id This data item is a pointer to attribute id in category em_buffer in the BUFFER category. em_sample_preparation.details Details on the sample preparation Selectively stained by injection of horseradish peroxidase, embedded in Spurr's resin and cut into 2-3 um thick sections. 1 Enzyme Preparations. S. cerevisiae PDC was purified to near homogeneity from baker's yeast by modification of a published procedure. Highly purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3 followed by FPLC on a Superdex 200 column. The weight-average molecular weight of the PDC was determined by light scattering measurement to be ~8 x 106. On the basis of the known molecular weight of the complex and its component enzymes and the experimentally determined polypeptide chain ratios of E2/BP/E3, we estimated that the subunit composition of the S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers, and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC preparation to increase the molar ratio of E1/E2 core to 60:1. This product is designated larger PDC or ~60 E1/E2 core PDC 2 embedment in vitreous ice. 3 Detergent-solubilized particles eluted from the cation-exchange column were directly adsorbed for 1 min to parlodion carbon-coated copper grids rendered hydrophilic by glow discharge at low pressure in air. Grids were washed with 4 drops of double-distilled water and stained with 2 drops of 0.75% uranyl formate. Images were recorded on Eastman Kodak Co. SO-163 sheet film with a Hitachi H-7000 electron microscope operated at 100 kV. Electron micrographs of single particles adsorbed to the carbon film were digitized using a Leafscan-45 scanner (Leaf Systems, Inc., Westborough, MA). 4 em_sample_preparation.entity_assembly_id This data item is a pointer to attribute id in category entity_assembly in the entity_assembly category. em_sample_preparation.ph The pH value of the observed sample buffer. 5.5 em_sample_preparation.sample_concentration The value of the concentration (mg per milliliter) of the complex in the sample. 1.35 em_sample_preparation.support_id This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. em_sample_preparation.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_sample_preparation.id The value of attribute id in category em_sample_preparation must uniquely identify the sample preparation. 0 em_sample_support Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_supportCategory> <PDBx:em_sample_support id="1"> <PDBx:citation_id>2</PDBx:citation_id> <PDBx:details xsi:nil="true" /> <PDBx:film_material>HOLEY CARBON</PDBx:film_material> <PDBx:grid_material>COPPER</PDBx:grid_material> <PDBx:grid_mesh_size>400</PDBx:grid_mesh_size> <PDBx:grid_type>MESH</PDBx:grid_type> <PDBx:method xsi:nil="true" /> <PDBx:pretreatment>GLOW DISCHARGE</PDBx:pretreatment> </PDBx:em_sample_support> </PDBx:em_sample_supportCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 em_sample_supportCategory This property indicates that datablock has a category holder em_sample_supportCategory. em_sample_supportCategory This property indicates that em_sample_supportCategory. has a category em_sample_support. em_sample_supportItem Abstract Datatype property for em_sample_support items. reference_to_em_sample_support cross-reference to em_sample_support referenced_by_em_sample_support cross-reference from em_sample_support em_sample_support.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. em_sample_support.details A description of any additional details concerning the sample support. This grid plus sample was kept at -170 deg C for a month before use CARBON FORMVAR PLUS CARBON CELLULOSE ACETATE PLUS CARBON PARLODION PLUS CARBON HOLEY CARBON The support material covering the em grid. COPPER COPPER/PALLADIUM COPPER/RHODIUM GOLD NICKEL PLATINUM TUNGSTEN TITANIUM MOLYBDENUM The name of the material from which the grid is made. em_sample_support.grid_mesh_size The value of the mesh size (per inch) of the em grid. 400 SLOT APERTURE DIAMOND HEXAGONAL A description of the grid type. em_sample_support.method A description of the method used to produce the support film. 1%formvar in chloroform cast on distilled water em_sample_support.pretreatment A description of the grid plus support film pretreatment. glow-discharged for 30 sec in argon em_sample_support.id The value of attribute id in category em_sample_support must uniquely identify the sample support. 0 em_single_particle_entity Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type. Example 1 - based on PDB entry 1EG0 <PDBx:em_single_particle_entityCategory> <PDBx:em_single_particle_entity entry_id="1EG0"> <PDBx:symmetry_type>ASYMMETRIC</PDBx:symmetry_type> </PDBx:em_single_particle_entity> </PDBx:em_single_particle_entityCategory> Example 2 - based on PDB entry 2ZLE <PDBx:em_single_particle_entityCategory> <PDBx:em_single_particle_entity entry_id="2ZLE"> <PDBx:symmetry_type>MIXED SYMMETRY</PDBx:symmetry_type> </PDBx:em_single_particle_entity> </PDBx:em_single_particle_entityCategory> 0 1 1 em_single_particle_entityCategory This property indicates that datablock has a category holder em_single_particle_entityCategory. em_single_particle_entityCategory This property indicates that em_single_particle_entityCategory. has a category em_single_particle_entity. em_single_particle_entityItem Abstract Datatype property for em_single_particle_entity items. reference_to_em_single_particle_entity cross-reference to em_single_particle_entity referenced_by_em_single_particle_entity cross-reference from em_single_particle_entity ASYMMETRIC CYCLIC DIHEDRAL TETRAHEDRAL OCTAHEDRAL ICOSAHEDRAL MIXED SYMMETRY The single particle symmetry type. em_single_particle_entity.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 em_virus_entity Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_virus_entityCategory> <PDBx:em_virus_entity entity_assembly_id="1" id="1"> <PDBx:empty>NO</PDBx:empty> <PDBx:enveloped>YES</PDBx:enveloped> <PDBx:ictvdb_id>00.073.0.01.023</PDBx:ictvdb_id> <PDBx:virus_host_category>VERTERBRATES</PDBx:virus_host_category> <PDBx:virus_host_species>HOMO SAPIENS</PDBx:virus_host_species> <PDBx:virus_isolate>STRAIN</PDBx:virus_isolate> <PDBx:virus_type>VIRUS</PDBx:virus_type> </PDBx:em_virus_entity> </PDBx:em_virus_entityCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_virus_entityCategory This property indicates that datablock has a category holder em_virus_entityCategory. em_virus_entityCategory This property indicates that em_virus_entityCategory. has a category em_virus_entity. em_virus_entityItem Abstract Datatype property for em_virus_entity items. reference_to_em_virus_entity cross-reference to em_virus_entity referenced_by_em_virus_entity cross-reference from em_virus_entity em_virus_entity.details Additional details about this virus entity YES NO Flag to indicate if the virus is empty or not. YES NO Flag to indicate if the virus is enveloped or not. em_virus_entity.ictvdb_id The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. NL-54 em_virus_entity.virus_host_category The host category description for the virus. ALGAE ARCHAEA BACTERIA(EUBACTERIA) FUNGI INVERTEBRATES PLANTAE (HIGHER PLANTS) PROTOZOA VERTEBRATES em_virus_entity.virus_host_growth_cell The host cell from which the virus was isolated. HELA CHO em_virus_entity.virus_host_species The host species from which the virus was isolated. homo sapiens gallus gallus STRAIN SEROTYPE SEROCOMPLEX SUBSPECIES SPECIES OTHER The isolate from which the virus was obtained. em_virus_entity.virus_type The type of virus. VIRION SATELLITE PRION VIROID VIRUS-LIKE PARTICLE em_virus_entity.entity_assembly_id This data item is a pointer to attribute id in category em_virus_entity in the ENTITY_ASSEMBLY category. em_virus_entity.id Is the unique identifier for VIRUS_ENTITY category. 0 em_vitrification Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_vitrificationCategory> <PDBx:em_vitrification entry_id="1DYL" id="1"> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:cryogen_name>ETHANE</PDBx:cryogen_name> <PDBx:details> SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER. </PDBx:details> <PDBx:humidity>90</PDBx:humidity> <PDBx:instrument xsi:nil="true" /> <PDBx:method>PLUNGE VITRIFICATION</PDBx:method> <PDBx:sample_preparation_id>1</PDBx:sample_preparation_id> <PDBx:temp>95</PDBx:temp> <PDBx:time_resolved_state xsi:nil="true" /> </PDBx:em_vitrification> </PDBx:em_vitrificationCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 em_vitrificationCategory This property indicates that datablock has a category holder em_vitrificationCategory. em_vitrificationCategory This property indicates that em_vitrificationCategory. has a category em_vitrification. em_vitrificationItem Abstract Datatype property for em_vitrification items. reference_to_em_vitrification cross-reference to em_vitrification referenced_by_em_vitrification cross-reference from em_vitrification em_vitrification.citation_id This data item is a pointer to attribute id in category citation in the CITATION category. HELIUM NITROGEN PROPANE ETHANE METHANE FREON 22 FREON 12 OTHER NONE This is the name of the cryogen. em_vitrification.details Any additional details relating to vitrification. Vitrification carried out in argon atmosphere. em_vitrification.humidity The humidity (%) in the vicinity of the vitrification process. 90 em_vitrification.instrument The type of instrument used in the vitrification process. Reichert plunger em_vitrification.method The procedure for vitrification. blot for 2 seconds before plunging em_vitrification.sample_preparation_id This data item is a pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category. em_vitrification.temp The temperature (in degrees Kelvin) at which vitrification took place. 4.2 em_vitrification.time_resolved_state The length of time after an event effecting the sample that vitrification was induced and a description of the event. 30 msec after spraying with effector em_vitrification.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. em_vitrification.id The value of attribute id in category em_vitrification must uniquely identify the vitrification procedure. 0 entity Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entityCategory> <PDBx:entity id="1"> <PDBx:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</PDBx:details> <PDBx:formula_weight>10916</PDBx:formula_weight> <PDBx:type>polymer</PDBx:type> </PDBx:entity> <PDBx:entity id="2"> <PDBx:details xsi:nil="true" /> <PDBx:formula_weight>762</PDBx:formula_weight> <PDBx:type>non-polymer</PDBx:type> </PDBx:entity> <PDBx:entity id="3"> <PDBx:details xsi:nil="true" /> <PDBx:formula_weight>18</PDBx:formula_weight> <PDBx:type>water</PDBx:type> </PDBx:entity> </PDBx:entityCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entityCategory This property indicates that datablock has a category holder entityCategory. entityCategory This property indicates that entityCategory. has a category entity. entityItem Abstract Datatype property for entity items. reference_to_entity cross-reference to entity referenced_by_entity cross-reference from entity entity.details A description of special aspects of the entity. entity.formula_weight Formula mass in daltons of the entity. entity.pdbx_description A description of the entity, with the name of the entity in parenthesis. Maps to PDB compound name. DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3') PROFLAVINE PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1)) entity.pdbx_ec Enzyme Commission (EC) number(s) 2.7.7.7 entity.pdbx_formula_weight_exptl Experimentally determined formula mass in daltons of the entity MASS SPEC Method used to determine attribute pdbx_formula_weight_exptl in category entity. MASS SPEC entity.pdbx_fragment Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN entity.pdbx_modification Description(s) of any chemical or post-translational modifications entity.pdbx_mutation Details about any entity mutation(s). Y31H DEL(298-323) entity.pdbx_number_of_molecules A place holder for the number of molecules of the entity in the entry. 1.0 2.0 3.0 entity.pdbx_parent_entity_id An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source. 1 2 3 entity.pdbx_target_id The value of attribute target_id in category entity points to a TARGETDB target idenitifier from which this entity was generated. nat man syn The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. polymer non-polymer macrolide water Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. entity.id The value of attribute id in category entity must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. 0 entity_keywords Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_keywordsCategory> <PDBx:entity_keywords entity_id="2"> <PDBx:text>natural product, inhibitor, reduced peptide</PDBx:text> </PDBx:entity_keywords> </PDBx:entity_keywordsCategory> 0 1 0 1 0 1 0 1 1 entity_keywordsCategory This property indicates that datablock has a category holder entity_keywordsCategory. entity_keywordsCategory This property indicates that entity_keywordsCategory. has a category entity_keywords. entity_keywordsItem Abstract Datatype property for entity_keywords items. reference_to_entity_keywords cross-reference to entity_keywords referenced_by_entity_keywords cross-reference from entity_keywords entity_keywords.pdbx_ec Enzyme Commission (EC) number(s) 2.7.7.7 entity_keywords.pdbx_fragment Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN entity_keywords.pdbx_mutation Entity mutation description(s). Y31H DEL(298-323) entity_keywords.text Keywords describing this entity. polypeptide natural product polysaccharide entity_keywords.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_link Data items in the ENTITY_LINK category give details about the links between entities. 0 1 1 1 1 1 0 1 0 1 1 entity_linkCategory This property indicates that datablock has a category holder entity_linkCategory. entity_linkCategory This property indicates that entity_linkCategory. has a category entity_link. entity_linkItem Abstract Datatype property for entity_link items. reference_to_entity_link cross-reference to entity_link referenced_by_entity_link cross-reference from entity_link entity_link.details A description of special aspects of a link between chemical components in the structure. entity_link.entity_id_1 The entity ID of the first of the two entities joined by the link. This data item is a pointer to attribute id in category entity in the ENTITY category. entity_link.entity_id_2 The entity ID of the second of the two entities joined by the link. This data item is a pointer to attribute id in category entity in the ENTITY category. entity_link.entity_seq_num_1 For a polymer entity, the sequence number in the first of the two entities containing the link. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. entity_link.entity_seq_num_2 For a polymer entity, the sequence number in the second of the two entities containing the link. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. entity_link.link_id This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 0 entity_name_com Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_name_comCategory> <PDBx:entity_name_com entity_id="1"> <PDBx:name>HIV-1 protease monomer</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="1"> <PDBx:name>HIV-1 PR monomer</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2"> <PDBx:name>acetyl-pepstatin</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2"> <PDBx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="3"> <PDBx:name>water</PDBx:name> </PDBx:entity_name_com> </PDBx:entity_name_comCategory> 0 1 1 entity_name_comCategory This property indicates that datablock has a category holder entity_name_comCategory. entity_name_comCategory This property indicates that entity_name_comCategory. has a category entity_name_com. entity_name_comItem Abstract Datatype property for entity_name_com items. reference_to_entity_name_com cross-reference to entity_name_com referenced_by_entity_name_com cross-reference from entity_name_com entity_name_com.name A common name for the entity. HIV protease monomer hemoglobin alpha chain 2-fluoro-1,4-dichloro benzene arbutin entity_name_com.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_name_sys Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_name_sysCategory> <PDBx:entity_name_sys entity_id="1"> <PDBx:name>EC 3.4.23.16</PDBx:name> </PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="2"> <PDBx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</PDBx:name> </PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="3"> <PDBx:name>water</PDBx:name> </PDBx:entity_name_sys> </PDBx:entity_name_sysCategory> 0 1 0 1 1 entity_name_sysCategory This property indicates that datablock has a category holder entity_name_sysCategory. entity_name_sysCategory This property indicates that entity_name_sysCategory. has a category entity_name_sys. entity_name_sysItem Abstract Datatype property for entity_name_sys items. reference_to_entity_name_sys cross-reference to entity_name_sys referenced_by_entity_name_sys cross-reference from entity_name_sys entity_name_sys.name The systematic name for the entity. hydroquinone-beta-D-pyranoside EC 2.1.1.1 2-fluoro-1,4-dichlorobenzene entity_name_sys.system The system used to generate the systematic name of the entity. Chemical Abstracts conventions enzyme convention Sigma catalog entity_name_sys.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_poly Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_polyCategory> <PDBx:entity_poly entity_id="1"> <PDBx:nstd_chirality>no</PDBx:nstd_chirality> <PDBx:nstd_linkage>no</PDBx:nstd_linkage> <PDBx:nstd_monomer>no</PDBx:nstd_monomer> <PDBx:type>polypeptide(L)</PDBx:type> <PDBx:type_details xsi:nil="true" /> </PDBx:entity_poly> </PDBx:entity_polyCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entity_polyCategory This property indicates that datablock has a category holder entity_polyCategory. entity_polyCategory This property indicates that entity_polyCategory. has a category entity_poly. entity_polyItem Abstract Datatype property for entity_poly items. reference_to_entity_poly cross-reference to entity_poly referenced_by_entity_poly cross-reference from entity_poly no n yes y A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in attribute type in category entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by attribute type in category entity_poly. no n yes y A flag to indicate whether the polymer contains at least one monomer that is not considered standard. entity_poly.number_of_monomers The number of monomers in the polymer. entity_poly.pdbx_seq_one_letter_code Chemical sequence expressed as string of one-letter amino acid codes. Modifications and non-standard amino acids are coded as X. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other entity_poly.pdbx_seq_one_letter_code_can Cannonical chemical sequence expressed as string of one-letter amino acid codes. Modifications are coded as the parent amino acid where possible. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD entity_poly.pdbx_strand_id The PDB strand/chain id(s) corresponding to this polymer entity. A B A,B,C entity_poly.pdbx_target_identifier The sequence's target identifier registered at target database. 356560 polypeptide(D) polypeptide(L) polydeoxyribonucleotide polyribonucleotide polysaccharide(D) polysaccharide(L) polydeoxyribonucleotide/polyribonucleotide hybrid cyclic-pseudo-peptide other The type of the polymer. entity_poly.type_details A description of special aspects of the polymer type. monomer Ala 16 is a D-amino acid the oligomer contains alternating RNA and DNA units entity_poly.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_poly_seq Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_poly_seqCategory> <PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></PDBx:entity_poly_seq> </PDBx:entity_poly_seqCategory> 0 1 1 1 1 entity_poly_seqCategory This property indicates that datablock has a category holder entity_poly_seqCategory. entity_poly_seqCategory This property indicates that entity_poly_seqCategory. has a category entity_poly_seq. entity_poly_seqItem Abstract Datatype property for entity_poly_seq items. reference_to_entity_poly_seq cross-reference to entity_poly_seq referenced_by_entity_poly_seq cross-reference from entity_poly_seq no n yes y A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. entity_poly_seq.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. entity_poly_seq.mon_id This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. entity_poly_seq.num The value of attribute num in category entity_poly_seq must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. 0 entity_src_gen Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_src_genCategory> <PDBx:entity_src_gen entity_id="1"> <PDBx:gene_src_common_name>HIV-1</PDBx:gene_src_common_name> <PDBx:gene_src_strain>NY-5</PDBx:gene_src_strain> <PDBx:host_org_common_name>bacteria</PDBx:host_org_common_name> <PDBx:host_org_genus>Escherichia</PDBx:host_org_genus> <PDBx:host_org_species>coli</PDBx:host_org_species> <PDBx:plasmid_name>pB322</PDBx:plasmid_name> </PDBx:entity_src_gen> </PDBx:entity_src_genCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entity_src_genCategory This property indicates that datablock has a category holder entity_src_genCategory. entity_src_genCategory This property indicates that entity_src_genCategory. has a category entity_src_gen. entity_src_genItem Abstract Datatype property for entity_src_gen items. reference_to_entity_src_gen cross-reference to entity_src_gen referenced_by_entity_src_gen cross-reference from entity_src_gen entity_src_gen.expression_system_id A unique identifier for the expression system. This should be extracted from a local list of expression systems. entity_src_gen.gene_src_common_name The common name of the natural organism from which the gene was obtained. man yeast bacteria entity_src_gen.gene_src_details A description of special aspects of the natural organism from which the gene was obtained. entity_src_gen.gene_src_dev_stage A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active. entity_src_gen.gene_src_genus The genus of the natural organism from which the gene was obtained. Homo Saccharomyces Escherichia entity_src_gen.gene_src_species The species of the natural organism from which the gene was obtained. sapiens cerevisiae coli entity_src_gen.gene_src_strain The strain of the natural organism from which the gene was obtained, if relevant. DH5a BMH 71-18 entity_src_gen.gene_src_tissue The tissue of the natural organism from which the gene was obtained. heart liver eye lens entity_src_gen.gene_src_tissue_fraction The subcellular fraction of the tissue of the natural organism from which the gene was obtained. mitochondria nucleus membrane entity_src_gen.host_org_common_name The common name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item be derived from attribute host_org_common_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express yeast bacteria entity_src_gen.host_org_details A description of special aspects of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would derived from attribute host_org_details in category entity_src_gen_express entity_src_gen.host_org_genus The genus of the organism that served as host for the production of the entity. Saccharomyces Escherichia entity_src_gen.host_org_species The species of the organism that served as host for the production of the entity. cerevisiae coli entity_src_gen.host_org_strain The strain of the organism in which the entity was expressed. Where full details of the protein production are available it would be expected that this item be derived from attribute host_org_strain in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express DH5a BMH 71-18 entity_src_gen.pdbx_description Information on the source which is not given elsewhere. entity_src_gen.pdbx_gene_src_atcc American Type Culture Collection tissue culture number. 6051 entity_src_gen.pdbx_gene_src_cell Cell type. ENDOTHELIAL entity_src_gen.pdbx_gene_src_cell_line The specific line of cells. HELA CELLS entity_src_gen.pdbx_gene_src_cellular_location Identifies the location inside (or outside) the cell. CYTOPLASM NUCLEUS entity_src_gen.pdbx_gene_src_fragment A domain or fragment of the molecule. CYTOPLASM NUCLEUS entity_src_gen.pdbx_gene_src_gene Identifies the gene. entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. entity_src_gen.pdbx_gene_src_organ Organized group of tissues that carries on a specialized function. KIDNEY LIVER PANCREAS entity_src_gen.pdbx_gene_src_organelle Organized structure within cell. MITOCHONDRIA entity_src_gen.pdbx_gene_src_plasmid The source plasmid. entity_src_gen.pdbx_gene_src_plasmid_name The source plasmid. entity_src_gen.pdbx_gene_src_scientific_name Scientific name of the organism. ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE entity_src_gen.pdbx_gene_src_variant Identifies the variant. DELTAH1DELTATRP entity_src_gen.pdbx_host_org_atcc Americal Tissue Culture Collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_culture_collection in category entity_src_gen_express entity_src_gen.pdbx_host_org_cell Cell type from which the gene is derived. Where entity.target_id is provided this should be derived from details of the target. ENDOTHELIAL entity_src_gen.pdbx_host_org_cell_line A specific line of cells used as the expression system. Where full details of the protein production are available it would be expected that this item would be derived from entity_src_gen_express.host_org_cell_line HELA entity_src_gen.pdbx_host_org_cellular_location Identifies the location inside (or outside) the cell which expressed the molecule. CYTOPLASM NUCLEUS entity_src_gen.pdbx_host_org_culture_collection Culture collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived somehwere, but exactly where is not clear. entity_src_gen.pdbx_host_org_gene Specific gene which expressed the molecule. HIV-1 POL GLNS7 U1A (2-98, Y31H, Q36R) entity_src_gen.pdbx_host_org_ncbi_taxonomy_id NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. entity_src_gen.pdbx_host_org_organ Specific organ which expressed the molecule. KIDNEY entity_src_gen.pdbx_host_org_organelle Specific organelle which expressed the molecule. MITOCHONDRIA entity_src_gen.pdbx_host_org_scientific_name The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_scientific_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express ESCHERICHIA COLI SACCHAROMYCES CEREVISIAE entity_src_gen.pdbx_host_org_strain The strain of the organism in which the entity was expressed. AR120 entity_src_gen.pdbx_host_org_tissue The specific tissue which expressed the molecule. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_tissue in category entity_src_gen_express heart liver eye lens entity_src_gen.pdbx_host_org_tissue_fraction The fraction of the tissue which expressed the molecule. mitochondria nucleus membrane entity_src_gen.pdbx_host_org_variant Variant of the organism used as the expression system. Where full details of the protein production are available it would be expected that this item be derived from entity_src_gen_express.host_org_variant or via attribute host_org_tax_id in category entity_src_gen_express TRP-LAC LAMBDA DE3 entity_src_gen.pdbx_host_org_vector Identifies the vector used. Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_name in category entity_src_gen_clone. PBIT36 PET15B PUC18 entity_src_gen.pdbx_host_org_vector_type Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_type in category entity_src_gen_express. COSMID PLASMID entity_src_gen.plasmid_details A description of special aspects of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute details in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. entity_src_gen.plasmid_name The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute name in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. pET3C pT123sab entity_src_gen.start_construct_id A pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct. entity_src_gen.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entity_src_nat Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_src_natCategory> <PDBx:entity_src_nat entity_id="2"> <PDBx:common_name>bacteria</PDBx:common_name> <PDBx:details> Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales.</PDBx:details> <PDBx:genus>Actinomycetes</PDBx:genus> </PDBx:entity_src_nat> </PDBx:entity_src_natCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 entity_src_natCategory This property indicates that datablock has a category holder entity_src_natCategory. entity_src_natCategory This property indicates that entity_src_natCategory. has a category entity_src_nat. entity_src_natItem Abstract Datatype property for entity_src_nat items. reference_to_entity_src_nat cross-reference to entity_src_nat referenced_by_entity_src_nat cross-reference from entity_src_nat entity_src_nat.common_name The common name of the organism from which the entity was isolated. man yeast bacteria entity_src_nat.details A description of special aspects of the organism from which the entity was isolated. entity_src_nat.genus The genus of the organism from which the entity was isolated. Homo Saccharomyces Escherichia entity_src_nat.pdbx_atcc Americal Tissue Culture Collection number. 6051 entity_src_nat.pdbx_cell A particular cell type. BHK-21 entity_src_nat.pdbx_cell_line The specific line of cells. HELA entity_src_nat.pdbx_cellular_location Identifies the location inside (or outside) the cell. entity_src_nat.pdbx_fragment A domain or fragment of the molecule. entity_src_nat.pdbx_ncbi_taxonomy_id NCBI Taxonomy identifier for the source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. entity_src_nat.pdbx_organ Organized group of tissues that carries on a specialized function. KIDNEY entity_src_nat.pdbx_organelle Organized structure within cell. MITOCHONDRIA entity_src_nat.pdbx_organism_scientific Scientific name of the organism of the natural source. BOS TAURUS SUS SCROFA ASPERGILLUS ORYZAE entity_src_nat.pdbx_plasmid_details Details about the plasmid. PLC28 DERIVATIVE entity_src_nat.pdbx_plasmid_name The plasmid containing the gene. pB322 entity_src_nat.pdbx_secretion Identifies the secretion from which the molecule was isolated. saliva urine venom entity_src_nat.pdbx_variant Identifies the variant. entity_src_nat.species The species of the organism from which the entity was isolated. sapiens cerevisiae coli entity_src_nat.strain The strain of the organism from which the entity was isolated. DH5a BMH 71-18 entity_src_nat.tissue The tissue of the organism from which the entity was isolated. heart liver eye lens entity_src_nat.tissue_fraction The subcellular fraction of the tissue of the organism from which the entity was isolated. mitochondria nucleus membrane entity_src_nat.entity_id This data item is a pointer to attribute id in category entity in the ENTITY category. 0 entry There is only one item in the ENTRY category, attribute id in category entry. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entryCategory> <PDBx:entry id="5HVP"></PDBx:entry> </PDBx:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:entryCategory> <PDBx:entry id="TOZ"></PDBx:entry> </PDBx:entryCategory> 0 1 0 1 1 entryCategory This property indicates that datablock has a category holder entryCategory. entryCategory This property indicates that entryCategory. has a category entry. entryItem Abstract Datatype property for entry items. reference_to_entry cross-reference to entry referenced_by_entry cross-reference from entry entry.pdbx_DOI Document Object Identifier (DOI) for this entry registered with http://crossref.org. entry.pdbx_pc Placeholder for additional parent-child relationships entry.id The value of attribute id in category entry identifies the data block. Note that this item need not be a number; it can be any unique identifier. 0 entry_link Data items in the ENTRY_LINK category record the relationships between the current data block identified by attribute id in category entry and other data blocks within the current file which may be referenced in the current data block. Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:entry_linkCategory> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_COM"> <PDBx:details>experimental data common to ref./mod. structures</PDBx:details> </PDBx:entry_link> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_REF"> <PDBx:details>reference structure</PDBx:details> </PDBx:entry_link> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_MOD"> <PDBx:details>modulated structure</PDBx:details> </PDBx:entry_link> </PDBx:entry_linkCategory> 0 1 1 1 entry_linkCategory This property indicates that datablock has a category holder entry_linkCategory. entry_linkCategory This property indicates that entry_linkCategory. has a category entry_link. entry_linkItem Abstract Datatype property for entry_link items. reference_to_entry_link cross-reference to entry_link referenced_by_entry_link cross-reference from entry_link entry_link.details A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. entry_link.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. entry_link.id The value of attribute id in category entry_link identifies a data block related to the current data block. 0 exptl Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <PDBx:exptlCategory> <PDBx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction"> <PDBx:absorpt_coefficient_mu>1.22</PDBx:absorpt_coefficient_mu> <PDBx:absorpt_correction_T_max>0.896</PDBx:absorpt_correction_T_max> <PDBx:absorpt_correction_T_min>0.802</PDBx:absorpt_correction_T_min> <PDBx:absorpt_correction_type>integration</PDBx:absorpt_correction_type> <PDBx:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</PDBx:absorpt_process_details> <PDBx:crystals_number>1</PDBx:crystals_number> <PDBx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</PDBx:details> <PDBx:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</PDBx:method_details> </PDBx:exptl> </PDBx:exptlCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 exptlCategory This property indicates that datablock has a category holder exptlCategory. exptlCategory This property indicates that exptlCategory. has a category exptl. exptlItem Abstract Datatype property for exptl items. reference_to_exptl cross-reference to exptl referenced_by_exptl cross-reference from exptl exptl.absorpt_coefficient_mu The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. exptl.absorpt_correction_T_max The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. exptl.absorpt_correction_T_min The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. analytical cylinder empirical gaussian integration multi-scan none numerical psi-scan refdelf sphere The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. exptl.absorpt_process_details Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. Tompa analytical exptl.crystals_number The total number of crystals used in the measurement of intensities. exptl.details Any special information about the experimental work prior to the intensity measurement. See also attribute preparation in category exptl_crystal. exptl.method_details A description of special aspects of the experimental method. 29 structures minimized average structure exptl.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION INFRARED SPECTROSCOPY EPR FLUORESCENCE TRANSFER THEORETICAL MODEL The method used in the experiment. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION 0 exptl_crystal Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:F_000>202</PDBx:F_000> <PDBx:colour>pale yellow</PDBx:colour> <PDBx:density_Matthews>1.01</PDBx:density_Matthews> <PDBx:density_diffrn>1.113</PDBx:density_diffrn> <PDBx:density_meas>1.11</PDBx:density_meas> <PDBx:density_meas_temp>294.5</PDBx:density_meas_temp> <PDBx:density_method>neutral buoyancy</PDBx:density_method> <PDBx:density_percent_sol>0.15</PDBx:density_percent_sol> <PDBx:description>hexagonal rod, uncut</PDBx:description> <PDBx:preparation> hanging drop, crystal soaked in 10&#37; ethylene glycol for 10 h, then placed in nylon loop at data collection time</PDBx:preparation> <PDBx:size_max>0.30</PDBx:size_max> <PDBx:size_mid>0.20</PDBx:size_mid> <PDBx:size_min>0.05</PDBx:size_min> <PDBx:size_rad>0.025</PDBx:size_rad> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> Example 2 - using separate items to define upper and lower limits for a value. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:density_meas_gt>2.5</PDBx:density_meas_gt> <PDBx:density_meas_lt>5.0</PDBx:density_meas_lt> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> Example 3 - here the density was measured at some unspecified temperature below room temperature. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:density_meas_temp_lt>300</PDBx:density_meas_temp_lt> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 exptl_crystalCategory This property indicates that datablock has a category holder exptl_crystalCategory. exptl_crystalCategory This property indicates that exptl_crystalCategory. has a category exptl_crystal. exptl_crystalItem Abstract Datatype property for exptl_crystal items. reference_to_exptl_crystal cross-reference to exptl_crystal referenced_by_exptl_crystal cross-reference from exptl_crystal exptl_crystal.F_000 The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 degree f~i~ = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell exptl_crystal.colour The colour of the crystal. dark green metallic dull clear The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. light dark whitish blackish grayish brownish reddish pinkish orangish yellowish greenish bluish The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. colourless white black gray brown red pink orange yellow green blue violet The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. exptl_crystal.density_Matthews The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. exptl_crystal.density_diffrn Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). exptl_crystal.density_meas Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). exptl_crystal.density_meas_esd The estimated standard deviation of attribute density_meas in category exptl_crystal. exptl_crystal.density_meas_gt The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which attribute density_meas in category exptl_crystal should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under attribute density_meas in category exptl_crystal. lower limit for the density (only the range within which the density lies was given in the original paper) 2.5 exptl_crystal.density_meas_lt The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which attribute density_meas in category exptl_crystal should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under attribute density_meas in category exptl_crystal. specimen floats in water 1.0 upper limit for the density (only the range within which the density lies was given in the original paper) 5.0 exptl_crystal.density_meas_temp Temperature in kelvins at which attribute density_meas in category exptl_crystal was determined. exptl_crystal.density_meas_temp_esd The estimated standard deviation of attribute density_meas_temp in category exptl_crystal. exptl_crystal.density_meas_temp_gt Temperature in kelvins above which attribute density_meas in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and attribute density_meas_temp_lt in category exptl_crystal should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under attribute density_meas_temp in category exptl_crystal. exptl_crystal.density_meas_temp_lt Temperature in kelvins below which attribute density_meas in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and attribute density_meas_temp_lt in category exptl_crystal should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under attribute density_meas_temp in category exptl_crystal. The density was measured at some unspecified temperature below room temperature. 300 exptl_crystal.density_method The method used to measure attribute density_meas in category exptl_crystal. exptl_crystal.density_percent_sol Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule exptl_crystal.description A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. exptl_crystal.pdbx_crystal_image_format The image format for the file containing the image of crystal specified as an RFC2045/RFC2046 mime type. jpeg gif tiff exptl_crystal.pdbx_crystal_image_url The URL for an a file containing the image of crystal. exptl_crystal.pdbx_mosaicity The of the distribution of mis-orientation angles specified in degrees of all the unit cells in the crystal. Lower mosaicity indicates better ordered crystals. exptl_crystal.pdbx_mosaicity_esd The uncertainty in the mosaicity estimate for the crystal. exptl_crystal.preparation Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. mounted in an argon-filled quartz capillary exptl_crystal.size_max The maximum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.size_mid The medial dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.size_min The minimum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.size_rad The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. exptl_crystal.id The value of attribute id in category exptl_crystal must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. 0 exptl_crystal_face Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4 for the 100 face of crystal xstl1. <PDBx:exptl_crystal_faceCategory> <PDBx:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0"> <PDBx:diffr_chi>42.56</PDBx:diffr_chi> <PDBx:diffr_kappa>30.23</PDBx:diffr_kappa> <PDBx:diffr_phi>-125.56</PDBx:diffr_phi> <PDBx:diffr_psi>-0.34</PDBx:diffr_psi> <PDBx:perp_dist>0.025</PDBx:perp_dist> </PDBx:exptl_crystal_face> </PDBx:exptl_crystal_faceCategory> 0 1 0 1 0 1 0 1 0 1 1 1 1 1 exptl_crystal_faceCategory This property indicates that datablock has a category holder exptl_crystal_faceCategory. exptl_crystal_faceCategory This property indicates that exptl_crystal_faceCategory. has a category exptl_crystal_face. exptl_crystal_faceItem Abstract Datatype property for exptl_crystal_face items. reference_to_exptl_crystal_face cross-reference to exptl_crystal_face referenced_by_exptl_crystal_face cross-reference from exptl_crystal_face exptl_crystal_face.diffr_chi The chi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.diffr_kappa The kappa diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.diffr_phi The phi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.diffr_psi The psi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.perp_dist The perpendicular distance in millimetres from the face to the centre of rotation of the crystal. exptl_crystal_face.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. exptl_crystal_face.index_h Miller index h of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.index_k Miller index k of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. exptl_crystal_face.index_l Miller index l of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. 0 exptl_crystal_grow Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:exptl_crystal_growCategory> <PDBx:exptl_crystal_grow crystal_id="1"> <PDBx:apparatus>Linbro plates</PDBx:apparatus> <PDBx:atmosphere>room air</PDBx:atmosphere> <PDBx:method>hanging drop</PDBx:method> <PDBx:pH>4.7</PDBx:pH> <PDBx:temp>18.</PDBx:temp> <PDBx:time>approximately 2 days</PDBx:time> </PDBx:exptl_crystal_grow> </PDBx:exptl_crystal_growCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 exptl_crystal_growCategory This property indicates that datablock has a category holder exptl_crystal_growCategory. exptl_crystal_growCategory This property indicates that exptl_crystal_growCategory. has a category exptl_crystal_grow. exptl_crystal_growItem Abstract Datatype property for exptl_crystal_grow items. reference_to_exptl_crystal_grow cross-reference to exptl_crystal_grow referenced_by_exptl_crystal_grow cross-reference from exptl_crystal_grow exptl_crystal_grow.apparatus The physical apparatus in which the crystal was grown. Linbro plate sandwich box ACA plates exptl_crystal_grow.atmosphere The nature of the gas or gas mixture in which the crystal was grown. room air nitrogen argon exptl_crystal_grow.details A description of special aspects of the crystal growth. Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. exptl_crystal_grow.method The method used to grow the crystals. batch precipitation batch dialysis hanging drop vapor diffusion sitting drop vapor diffusion exptl_crystal_grow.method_ref A literature reference that describes the method used to grow the crystals. McPherson et al., 1988 exptl_crystal_grow.pH The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in attribute details in category exptl_crystal_grow. 7.4 7.6 4.3 exptl_crystal_grow.pdbx_details Text description of crystal grow procedure. PEG 4000, potassium phosphate, magnesium chloride, cacodylate exptl_crystal_grow.pdbx_pH_range The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. 5.6 - 6.4 exptl_crystal_grow.pressure The ambient pressure in kilopascals at which the crystal was grown. exptl_crystal_grow.pressure_esd The standard uncertainty (estimated standard deviation) of attribute pressure in category exptl_crystal_grow. exptl_crystal_grow.seeding A description of the protocol used for seeding the crystal growth. macroseeding Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. exptl_crystal_grow.seeding_ref A literature reference that describes the protocol used to seed the crystal. Stura et al., 1989 exptl_crystal_grow.temp The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in attribute details in category exptl_crystal_grow. exptl_crystal_grow.temp_details A description of special aspects of temperature control during crystal growth. exptl_crystal_grow.temp_esd The standard uncertainty (estimated standard deviation) of attribute temp in category exptl_crystal_grow. exptl_crystal_grow.time The approximate time that the crystal took to grow to the size used for data collection. overnight 2-4 days 6 months exptl_crystal_grow.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. 0 exptl_crystal_grow_comp Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in attribute details in category exptl_crystal_grow_comp using the solutions described in EXPTL_CRYSTAL_GROW_COMP. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:exptl_crystal_grow_compCategory> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="1"> <PDBx:conc>6 mg/ml</PDBx:conc> <PDBx:details> The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</PDBx:details> <PDBx:name>HIV-1 protease</PDBx:name> <PDBx:sol_id>1</PDBx:sol_id> <PDBx:volume>0.002 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="2"> <PDBx:conc>4 M</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>NaCl</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.200 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="3"> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.047 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="4"> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details> in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured.</PDBx:details> <PDBx:name>Na Acetate</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.053 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="5"> <PDBx:conc>neat</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>water</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.700 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> </PDBx:exptl_crystal_grow_compCategory> 0 1 0 1 0 1 0 1 0 1 1 1 exptl_crystal_grow_compCategory This property indicates that datablock has a category holder exptl_crystal_grow_compCategory. exptl_crystal_grow_compCategory This property indicates that exptl_crystal_grow_compCategory. has a category exptl_crystal_grow_comp. exptl_crystal_grow_compItem Abstract Datatype property for exptl_crystal_grow_comp items. reference_to_exptl_crystal_grow_comp cross-reference to exptl_crystal_grow_comp referenced_by_exptl_crystal_grow_comp cross-reference from exptl_crystal_grow_comp exptl_crystal_grow_comp.conc The concentration of the solution component. 200 \ml 0.1 ml exptl_crystal_grow_comp.details A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. in 3 mM NaAzide The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. exptl_crystal_grow_comp.name A common name for the component of the solution. protein in buffer acetic acid exptl_crystal_grow_comp.sol_id An identifier for the solution to which the given solution component belongs. 1 well solution solution A exptl_crystal_grow_comp.volume The volume of the solution component. 200 \ml 0.1 ml exptl_crystal_grow_comp.crystal_id This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. exptl_crystal_grow_comp.id The value of attribute id in category exptl_crystal_grow_comp must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. 1 A protein in buffer 0 geom Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag. 0 1 1 geomCategory This property indicates that datablock has a category holder geomCategory. geomCategory This property indicates that geomCategory. has a category geom. geomItem Abstract Datatype property for geom items. reference_to_geom cross-reference to geom referenced_by_geom cross-reference from geom geom.details A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes. geom.entry_id This data item is a pointer to attribute id in category entry in the ENTRY category. 0 geom_angle Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:geom_angleCategory> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>111.6</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>110.9</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>122.2</PDBx:value> <PDBx:value_esd>0.3</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>127.0</PDBx:value> <PDBx:value_esd>0.3</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>101.3</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>111.3</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>107</PDBx:value> <PDBx:value_esd>1</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>116.7</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> </PDBx:geom_angleCategory> 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 1 1 1 1 1 geom_angleCategory This property indicates that datablock has a category holder geom_angleCategory. geom_angleCategory This property indicates that geom_angleCategory. has a category geom_angle. geom_angleItem Abstract Datatype property for geom_angle items. reference_to_geom_angle cross-reference to geom_angle referenced_by_geom_angle cross-reference from geom_angle geom_angle.atom_site_auth_asym_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_asym_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_asym_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_atom_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_atom_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_atom_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_comp_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_comp_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_comp_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_seq_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_seq_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_auth_seq_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_alt_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_alt_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_alt_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_asym_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_asym_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_asym_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_atom_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_atom_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_atom_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_comp_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_comp_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_comp_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_seq_id_1 An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_seq_id_2 An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_label_seq_id_3 An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. geom_angle.pdbx_PDB_model_num Pointer to attribute pdbx_PDB_model_num in category atom_site geom_angle.pdbx_atom_site_PDB_ins_code_1 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_angle.pdbx_atom_site_PDB_ins_code_2 Pointer to attribute pdbx_PDB_ins_code in category atom_site. geom_angle.pdbx_atom_site_PDB_ins_code_3 Pointer to attribute pdbx_PDB_ins_code in category atom_site. no n yes y This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. geom_angle.value Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and attribute atom_site_id_3 in category geom_angle. geom_angle.value_esd The standard uncertainty (estimated standard deviation) of attribute value in category geom_angle. geom_angle.atom_site_id_1 The identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_id_2 The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_angle.atom_site_id_3 The identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. geom_angle.site_symmetry_1 The symmetry code of the first of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_angle.site_symmetry_2 The symmetry code of the second of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 geom_angle.site_symmetry_3 The symmetry code of the third of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 0 geom_bond Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:geom_bondCategory> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.342</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.439</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.512</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.199</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.465</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.537</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.00</PDBx:dist> <PDBx:dist_esd>0.03</PDBx:dist_esd> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.472</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> </PDBx:geom_bondCategory>