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- PDB-1n8r: Structure of large ribosomal subunit in complex with virginiamycin M -

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Basic information

Entry
Database: PDB / ID: 1n8r
TitleStructure of large ribosomal subunit in complex with virginiamycin M
Components
  • (50S ribosomal protein ...) x 27
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Acidic ribosomal protein P0 homolog
KeywordsRibosome/Antibiotic / ribosome-antibiotic complex / virginiamycin M / streptogramin / antibiotic
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / DNA repair / nucleotide binding / mRNA binding / 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 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / 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 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / 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 L31e; Chain: W; / Ribosomal protein L31 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / Helix Hairpins - #310 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / 50S ribosomal protein L10, archaea / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, 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 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L30; Chain: A, / SH3 type barrels. - #30 / : / Ribosomal protein L30/S12 / Ribosomal Protein L22; Chain A / Ribosomal protein L7Ae, archaea / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / : / N-terminal domain of TfIIb / Translation factors / Helix-hairpin-helix domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Single Sheet / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
: / : / VIRGINIAMYCIN M1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...: / : / VIRGINIAMYCIN M1 / : / 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 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHansen, J.L. / Moore, P.B. / Steitz, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit
Authors: Hansen, J. / Moore, P.B. / Steitz, T.A.
#1: Journal: Science / Year: 2000
Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
#2: Journal: Science / Year: 2000
Title: The structural basis of ribosome activity in peptide bond synthesis
Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2P
D: 50S ribosomal protein L3P
E: 50S ribosomal protein L4E
F: 50S ribosomal protein L5P
G: 50S ribosomal protein L6P
H: 50S ribosomal protein L7Ae
I: Acidic ribosomal protein P0 homolog
J: 50S ribosomal protein L10e
K: 50S ribosomal protein L13P
L: 50S ribosomal protein L14P
M: 50S ribosomal protein L15P
N: 50S ribosomal protein L15E
O: 50S ribosomal protein L18P
P: 50S ribosomal protein L18E
Q: 50S ribosomal protein L19E
R: 50S ribosomal protein L21e
S: 50S ribosomal protein L22P
T: 50S ribosomal protein L23P
U: 50S ribosomal protein L24P
V: 50S ribosomal protein L24E
W: 50S ribosomal protein L29P
X: 50S ribosomal protein L30P
Y: 50S ribosomal protein L31E
Z: 50S ribosomal protein L32E
1: 50S ribosomal protein L37AE
2: 50S ribosomal protein L37e
3: 50S ribosomal protein L39e
4: 50S ribosomal protein L44E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,458,642262
Polymers1,451,91430
Non-polymers6,728232
Water141,9947882
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.902, 300.474, 575.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA


Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#2: RNA chain 5S ribosomal RNA


Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779

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50S ribosomal protein ... , 27 types, 27 molecules CDEFGHJKLMNOPQRSTUVWXYZ1234

#3: Protein 50S ribosomal protein L2P / Hmal2 / HL4


Mass: 25237.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#4: Protein 50S ribosomal protein L3P / Hmal3 / HL1


Mass: 37265.195 Da / Num. of mol.: 1 / Mutation: R310P, 311F insertion / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#5: Protein 50S ribosomal protein L4E / Hmal4 / HL6


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#6: Protein 50S ribosomal protein L5P / Hmal5 / HL13


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#7: Protein 50S ribosomal protein L6P / Hmal6 / HL10


Mass: 19830.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#8: Protein 50S ribosomal protein L7Ae / HS6


Mass: 12600.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#10: Protein 50S ribosomal protein L10e


Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617*PLUS
#11: Protein 50S ribosomal protein L13P / Hmal13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#12: Protein 50S ribosomal protein L14P / Hmal14 / HL27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#13: Protein 50S ribosomal protein L15P / Hmal15 / HL9


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#14: Protein 50S ribosomal protein L15E


Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618*PLUS
#15: Protein 50S ribosomal protein L18P / Hmal18 / HL12


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#16: Protein 50S ribosomal protein L18E / HL29 / L19


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#17: Protein 50S ribosomal protein L19E / Hmal19 / HL24


Mass: 16631.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#18: Protein 50S ribosomal protein L21e / HL31


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#19: Protein 50S ribosomal protein L22P / Hmal22 / HL23


Mass: 16835.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#20: Protein 50S ribosomal protein L23P / Hmal23 / HL25 / L21


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#21: Protein 50S ribosomal protein L24P / Hmal24 / HL16 / HL15


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#22: Protein 50S ribosomal protein L24E / HL21/HL22


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#23: Protein 50S ribosomal protein L29P / Hmal29 / HL33


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#24: Protein 50S ribosomal protein L30P / Hmal30 / HL20 / HL16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#25: Protein 50S ribosomal protein L31E / L34 / HL30


Mass: 10253.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#26: Protein 50S ribosomal protein L32E / HL5


Mass: 26324.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#27: Protein 50S ribosomal protein L37AE


Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#28: Protein 50S ribosomal protein L37e / L35e


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#29: Protein/peptide 50S ribosomal protein L39e / HL39e / HL46e


Mass: 5844.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#30: Protein 50S ribosomal protein L44E / LA / HLA


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

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Protein , 1 types, 1 molecules I

#9: Protein Acidic ribosomal protein P0 homolog / L10E / HMaL10


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825

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Non-polymers , 7 types, 8114 molecules

#31: Chemical ChemComp-VIR / VIRGINIAMYCIN M1


Mass: 525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N3O7
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#34: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Na
#35: Chemical...
ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 7882 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.2M KCl, 0.5M (NH4)Cl, 30mM MgCl2, 8% PEG, pH 5.80, VAPOR DIFFUSION, SITTING DROP at 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2NH4Cl11
3MgCl211
4PEG 600011
5KCl12
6NH4Cl12
7MgCl212
8PEG 600012
Crystal grow
*PLUS
pH: 7.1 / Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 M1reservoirKCl
20.5 M1reservoirNH4Cl
3100 mMpotassium acetate1reservoir
430 mM1reservoirMgCl2
57 %PEG60001reservoir
615 mMTris1reservoir
715 mMMES1reservoir
81 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0332 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 344322 / Num. obs: 339727 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / Num. unique all: 16729 / Rsym value: 0.49 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 3 Å / % possible obs: 94.6 % / Redundancy: 4 %
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 37.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJ2

1jj2


Resolution: 3→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3203 1 %same reflections as 1JJ2
Rwork0.201 ---
obs0.2011 327972 94.6 %-
all-346861 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7669 Å2 / ksol: 0.329291 e/Å3
Displacement parametersBiso mean: 43.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2--1.7 Å20 Å2
3----6.84 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.54 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28801 61617 269 7882 98569
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d15.6
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it2.022.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 131 1 %
Rwork0.338 13488 -
obs--37.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1RNA.PARRNA.TOP
X-RAY DIFFRACTION2PROT.PARPROT.TOP
X-RAY DIFFRACTION3ION.PARION.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å

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