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- PDB-1aym: HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1aym
TitleHUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION
Components(HUMAN RHINOVIRUS 16 COAT ...) x 4
KeywordsVIRUS / HUMAN RHINOVIRUS 16 / RNA / SITE-DIRECTED MUTAGENESIS / RHINOVIRUS COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / MYRISTIC ACID / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR / Resolution: 2.15 Å
AuthorsHadfield, A.T. / Rossmann, M.G.
Citation
Journal: Structure / Year: 1997
Title: The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.
Authors: Hadfield, A.T. / Lee, W. / Zhao, R. / Oliveira, M.A. / Minor, I. / Rueckert, R.R. / Rossmann, M.G.
#1: Journal: Structure / Year: 1993
Title: The Structure of Human Rhinovirus 16
Authors: Oliveira, M.A. / Zhao, R. / Lee, W.M. / Kremer, M.J. / Minor, I. / Rueckert, R.R. / Diana, G.D. / Pevear, D.C. / Dutko, F.J. / Mckinlay, M.A. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A
Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / Dutko, F.J. / Mckinlay, M.A. / Pevear, D.C.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Structure of a Human Rhinovirus Complexed with its Receptor Molecule
Authors: Olson, N.H. / Kolatkar, P.R. / Oliveira, M.A. / Cheng, R.H. / Greve, J.M. / Mcclelland, A. / Baker, T.S. / Rossmann, M.G.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
Authors: Kim, S.S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A.
#5: Journal: Trends Biochem.Sci. / Year: 1987
Title: Common Cold Viruses
Authors: Rossmann, M.G. / Arnold, E. / Griffith, J.P. / Kamer, G. / Luo, M. / Smith, T.J. / Vriend, G. / Rueckert, R.R. / Sherry, B. / Mckinlay, M.A. / Diana, G. / Otto, M.
#6: Journal: Science / Year: 1986
Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J.
#7: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionNov 6, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms / struct_conn
Item: _pdbx_database_status.process_site
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_mon_prot_cis
Item: _struct_mon_prot_cis.pdbx_omega_angle

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6747
Polymers95,1804
Non-polymers4943
Water9,602533
1
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,740,457420
Polymers5,710,811240
Non-polymers29,646180
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 478 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)478,37135
Polymers475,90120
Non-polymers2,47015
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 574 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)574,04642
Polymers571,08124
Non-polymers2,96518
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.87 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,870,228210
Polymers2,855,405120
Non-polymers14,82390
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)362.600, 347.100, 334.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5, 0.25544312, 0.8274955), (0.3612676, 0.80687821, -0.46736845), (-0.78707414, 0.53263155, 0.31115577)45.3227, -32.74724, 71.34464
3generate(-0.30901699, 0.77458326, 0.5518417), (0.83998638, 0.49440059, -0.22358649), (-0.44601722, 0.39444749, -0.80341758)118.65636, -76.14089, 40.4294
4generate(-0.30901699, 0.83998639, -0.44601722), (0.77458326, 0.49440059, 0.39444749), (0.5518417, -0.22358649, -0.80341758)118.65636, -70.2124, -50.02191
5generate(0.5, 0.36126761, -0.78707414), (0.25544312, 0.80687821, 0.53263155), (0.8274955, -0.46736846, 0.31115577)45.3227, -23.15474, -75.00865
6generate(-0.80901699, 0.51914014, -0.27565379), (0.51914014, 0.41115427, -0.74929678), (-0.2756538, -0.74929679, -0.60213728)163.97905, -47.05766, 24.98675
7generate(0.06540313, -0.99785892), (0.99785892, 0.0652631, 0.00427757), (0.06540313, -0.99572244, -0.0652631)90.64539, -90.45131, -5.92849
8generate(0.80901699, -0.47871879, -0.34105692), (0.51914014, 0.30983393, 0.79655284), (-0.2756538, -0.82148114, 0.49918305)17.31173, -47.05766, 24.98675
9generate(0.5, -0.36126761, 0.78707414), (-0.25544312, 0.80687821, 0.53263155), (-0.8274955, -0.46736846, 0.31115577)45.3227, 23.15474, 75.00865
10generate(-0.5, 0.25544312, 0.8274955), (-0.25544312, 0.86949762, -0.42275607), (-0.8274955, -0.42275607, -0.36949762)135.96809, 23.15474, 75.00865
11generate(0.30901699, -0.77458326, -0.5518417), (-0.77458326, -0.54165665, 0.32654071), (-0.5518417, 0.32654071, -0.76736033)62.63442, 70.2124, 50.02191
12generate(0.30901699, -0.83998639, 0.44601722), (-0.83998638, -0.46098703, -0.2862059), (0.44601722, -0.2862059, -0.84802996)62.63442, 76.14089, -40.4294
13generate(-0.5, -0.36126761, 0.78707414), (-0.3612676, -0.73897143, -0.56868879), (0.78707414, -0.56868879, 0.23897142)135.96809, 32.74724, -71.34464
14generate(-1), (-0.99144486, -0.13052619), (-0.13052619, 0.99144486)181.29078
15generate(-0.5, -0.25544312, -0.8274955), (-0.25544312, -0.86949762, 0.42275607), (-0.8274955, 0.42275607, 0.36949762)135.96809, 23.15474, 75.00865
16generate(-0.99785893, -0.06540313), (-0.06540313, 0.0652631, -0.99572242), (0.99785892, 0.00427757, -0.0652631)90.64539, 5.92849, -90.45131
17generate(-0.30901699, -0.83998639, 0.44601722), (0.77458326, -0.49440059, -0.39444749), (0.5518417, 0.22358649, 0.80341758)118.65636, -70.2124, -50.02191
18generate(-0.80901699, -0.51914014, 0.27565379), (0.51914014, -0.41115427, 0.74929678), (-0.2756538, 0.74929679, 0.60213728)163.97905, -47.05766, 24.98675
19generate(-0.80901699, -0.47871879, -0.34105692), (-0.47871878, 0.19995846, 0.85489469), (-0.34105693, 0.8548947, -0.39094146)163.97905, 43.39365, 30.91524
20generate(-0.30901699, -0.77458326, -0.5518417), (-0.83998638, 0.49440059, -0.22358649), (0.44601722, 0.39444749, -0.80341758)118.65636, 76.14089, -40.4294
21generate(0.80901699, 0.51914014, -0.27565379), (0.47871878, -0.30983393, 0.82148113), (0.34105693, -0.79655285, -0.49918306)17.31173, -43.39365, -30.91524
22generate(0.80901699, 0.47871879, 0.34105692), (-0.51914014, 0.30983393, 0.79655284), (0.2756538, -0.82148114, 0.49918305)17.31173, 47.05766, -24.98675
23generate(0.30901699, 0.77458326, 0.5518417), (-0.77458326, 0.54165665, -0.32654071), (-0.5518417, -0.32654071, 0.76736033)62.63442, 70.2124, 50.02191
24generate(0.99785893, 0.06540313), (0.06540313, 0.0652631, -0.99572242), (-0.99785892, 0.00427757, -0.0652631)90.64539, -5.92849, 90.45131
25generate(0.30901699, 0.83998639, -0.44601722), (0.83998638, -0.46098703, -0.2862059), (-0.44601722, -0.2862059, -0.84802996)62.63442, -76.14089, 40.4294
26generate(-0.5, 0.36126761, -0.78707414), (-0.3612676, 0.73897143, 0.56868879), (0.78707414, 0.56868879, -0.23897142)135.96809, 32.74724, -71.34464
27generate(0.5, -0.25544312, -0.8274955), (-0.3612676, 0.80687821, -0.46736845), (0.78707414, 0.53263155, 0.31115577)45.3227, 32.74724, -71.34464
28generate(0.80901699, -0.51914014, 0.27565379), (0.47871878, 0.30983393, -0.82148113), (0.34105693, 0.79655285, 0.49918306)17.31173, -43.39365, -30.91524
29generate(-0.06540313, 0.99785892), (0.99785892, -0.0652631, -0.00427757), (0.06540313, 0.99572244, 0.0652631)90.64539, -90.45131, -5.92849
30generate(-0.80901699, 0.47871879, 0.34105692), (0.47871878, 0.19995846, 0.85489469), (0.34105693, 0.8548947, -0.39094146)163.97905, -43.39365, -30.91524

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Components

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HUMAN RHINOVIRUS 16 COAT ... , 4 types, 4 molecules 1234

#1: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 32501.375 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: Q82122
#2: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 28990.615 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: Q82122
#3: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 26314.168 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: Q82122
#4: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 7374.025 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: P23008

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Non-polymers , 4 types, 536 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlvirus1drop
20.25-0.75 %PEG80001drop
30.5-1.5 %PEG80001reservoir
45-20 mM1reservoirCaCl2
51reservoirNaCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 1452910 / % possible obs: 44.5 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.14→2.25 Å / Rmerge(I) obs: 0.24 / % possible all: 47
Reflection
*PLUS
Num. measured all: 3442752
Reflection shell
*PLUS
% possible obs: 47 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR
Starting model: PDB ENTRY 2RHN

2rhn
PDB Unreleased entry


Resolution: 2.15→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: DISORDERED SIDE CHAINS (1 1, 1 4, 1 5, 2 159, 2 160) WERE MODELLED WITH PREFERRED ROTAMERS WITH GOOD STEREOCHEMISTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 12388 10 %RANDOM
Rwork0.23 ---
obs0.23 1115369 44.5 %-
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 30 541 6954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22.5
Refine LS restraints NCSNCS model details: 30-FOLD, STRICT
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.298 9613 10 %
Rwork0.293 86834 -
obs--47 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR.AHTOP.AH
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.293

+
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