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- PDB-3g6e: Co-crystal structure of Homoharringtonine bound to the large ribo... -

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Basic information

Entry
Database: PDB / ID: 3g6e
TitleCo-crystal structure of Homoharringtonine bound to the large ribosomal subunit
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / large ribosomal subunit / antibiotic specificity / homoharringtonine / Haloarcula marismortui / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Metal-binding / Zinc-finger
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L19e, archaeal / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Helix-hairpin-helix domain / 50S ribosomal protein L10, insertion domain superfamily / Translation factors / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / RRM (RNA recognition motif) domain / Ribosomal protein L6, conserved site-2 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L39e, conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e
Similarity search - Domain/homology
: / Chem-HMT / : / STRONTIUM ION / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / Chem-HMT / : / STRONTIUM ION / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsGurel, G. / Blaha, G. / Moore, P.B. / Steitz, T.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
Authors: Gurel, G. / Blaha, G. / Moore, P.B. / Steitz, T.A.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 18, 2015Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S ribosomal RNA
A: 50S ribosomal protein L2P
B: 50S ribosomal protein L3P
C: 50S ribosomal protein L4P
D: 50S ribosomal protein L5P
E: 50S ribosomal protein L6P
F: 50S ribosomal protein L7Ae
G: 50S ribosomal protein L10E
H: 50S ribosomal protein L10e
I: 50S ribosomal protein L11P
J: 50S ribosomal protein L13P
K: 50S ribosomal protein L14P
L: 50S ribosomal protein L15P
M: 50S ribosomal protein L15e
N: 50S ribosomal protein L18P
O: 50S ribosomal protein L18e
P: 50S ribosomal protein L19e
Q: 50S ribosomal protein L21e
R: 50S ribosomal protein L22P
S: 50S ribosomal protein L23P
T: 50S ribosomal protein L24P
U: 50S ribosomal protein L24e
V: 50S ribosomal protein L29P
W: 50S ribosomal protein L30P
X: 50S ribosomal protein L31e
Y: 50S ribosomal protein L32e
Z: 50S ribosomal protein L37Ae
1: 50S ribosomal protein L37e
2: 50S ribosomal protein L39e
3: 50S ribosomal protein L44E
9: 5S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,461,627337
Polymers1,446,21431
Non-polymers15,413306
Water140,9317823
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.863, 299.418, 574.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsBIOLOGICAL UNIT IS THE SAME AS THE ASYMMETRIC UNIT.

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Components

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RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S ribosomal RNA /


Mass: 946463.500 Da / Num. of mol.: 1 / Fragment: Residues 2634210-2637132 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 55229667
#31: RNA chain 5S ribosomal RNA /


Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 6468293

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50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123

#2: Protein 50S ribosomal protein L2P / Ribosome / Hmal2 / Hl4


Mass: 24980.275 Da / Num. of mol.: 1 / Fragment: Residues 143-264 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#3: Protein 50S ribosomal protein L3P / Ribosome / Hmal3 / Hl1


Mass: 37265.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#4: Protein 50S ribosomal protein L4P / Ribosome / Hmal4 / Hl6


Mass: 26457.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#5: Protein 50S ribosomal protein L5P / Ribosome / Hmal5 / Hl13


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#6: Protein 50S ribosomal protein L6P / Ribosome / Hmal6 / Hl10


Mass: 19316.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#7: Protein 50S ribosomal protein L7Ae / Ribosome / Hs6


Mass: 12660.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#8: Protein 50S ribosomal protein L10E / Ribosome / Ribosomal protein L10 / Acidic ribosomal protein P0 homolog / L10E / HMal10


Mass: 37169.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825
#9: Protein 50S ribosomal protein L10e / Ribosome


Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617
#10: Protein 50S ribosomal protein L11P / Ribosome / Hmal11


Mass: 7408.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14122
#11: Protein 50S ribosomal protein L13P / Ribosome / Hmal13


Mass: 15931.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#12: Protein 50S ribosomal protein L14P / Ribosome / Hmal14 / Hl27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#13: Protein 50S ribosomal protein L15P / Ribosome / Hmal15 / Hl9


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#14: Protein 50S ribosomal protein L15e / Ribosome / 50S ribosomal protein LC12


Mass: 22143.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618
#15: Protein 50S ribosomal protein L18P / Ribosome / Hmal18 / Hl12


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#16: Protein 50S ribosomal protein L18e / Ribosome / Hl29 / L19


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#17: Protein 50S ribosomal protein L19e / Ribosome / Hmal19 / Hl24


Mass: 16169.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#18: Protein 50S ribosomal protein L21e / Ribosome / Hl31


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#19: Protein 50S ribosomal protein L22P / Ribosome / Hmal22 / Hl23


Mass: 16363.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#20: Protein 50S ribosomal protein L23P / Ribosome / Hmal23 / Hl25 / L21


Mass: 9177.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#21: Protein 50S ribosomal protein L24P / Ribosome / Hmal24 / Hl16 / Hl15


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#22: Protein 50S ribosomal protein L24e / Ribosome / Hl21/Hl22


Mass: 5919.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#23: Protein 50S ribosomal protein L29P / Ribosome / Hmal29 / Hl33


Mass: 7145.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#24: Protein 50S ribosomal protein L30P / Ribosome / Hmal30 / Hl20 / Hl16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#25: Protein 50S ribosomal protein L31e / Ribosome / L34 / Hl30


Mass: 9315.513 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#26: Protein 50S ribosomal protein L32e / Ribosome / Hl5


Mass: 16078.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#27: Protein 50S ribosomal protein L37Ae / Ribosome


Mass: 8224.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619
#28: Protein 50S ribosomal protein L37e / Ribosome / L35e


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#29: Protein/peptide 50S ribosomal protein L39e / Ribosome / Hl39e / Hl46e


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#30: Protein 50S ribosomal protein L44E / Ribosome / La / Hla


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411

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Non-polymers , 8 types, 8129 molecules

#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#34: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: Na
#35: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#36: Chemical...
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Sr
#37: Chemical ChemComp-HMT / (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine / Homoharringtonine / Cephalotaxine / [3(R)]-4-methyl 2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate / Omacetaxine mepesuccinate


Mass: 545.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H39NO9 / Comment: anticancer, alkaloid*YM
#38: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#39: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7823 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 6000, KCl, NH4Cl, MgCl2, pH 5.80, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NH4Cl11
4MgCl211
5PEG 600012
6KCl12
7NH4Cl12
8MgCl212

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11
SYNCHROTRONNSLS X29A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 29, 2007
ADSC QUANTUM 3152CCDMar 29, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 520043 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.075 / Χ2: 1.042 / Net I/σ(I): 17.792
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.65-2.743.3505961.099197.5
2.74-2.854.2519021.092199.90.753
2.85-2.985.4519581.08711000.487
2.98-3.145.6520421.04211000.269
3.14-3.345.6520911.00811000.155
3.34-3.65.6521641.01311000.102
3.6-3.965.5521281.0511000.067
3.96-4.535.5523011.009199.90.049
4.53-5.715.5523341.016199.60.049
5.71-505.4525271.044198.30.035

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3CC2

3cc2


Resolution: 2.7→49.9 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 226606 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4565 1 %RANDOM
Rwork0.19 ---
obs-464427 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.604 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 200 Å2 / Biso mean: 60.601 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-5.63 Å20 Å20 Å2
2---1.27 Å20 Å2
3----4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29387 61620 344 7823 99174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.3
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.482
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 674 1 %
Rwork0.331 66262 -
all-66936 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2dna-rna-joe-martin_comb_mnt.par&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5homo_8.PAR&_1_TOPOLOGY_INFILE_5

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