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- PDB-1sm1: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURA... -

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Basic information

Entry
Database: PDB / ID: 1sm1
TitleCOMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN
Components
  • (50S RIBOSOMAL PROTEIN ...) x 28
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • GENERAL STRESS PROTEIN CTC
  • QUINUPRISTIN
KeywordsRIBOSOME/ANTIBIOTIC / RIBOSOME-ANTIBIOTIC COMPLEX / QUINUPRISTIN / DALFOPRISTIN / STREPTOGRAMINS / SYNERCID / RIBOSOME / 50S RIBOSOMAL SUBUNIT / RIBOSOM-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome ...large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4
Similarity search - Domain/homology
Quinupristin / Chem-DOL / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 ...Quinupristin / Chem-DOL / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
STREPTOMYCES GRAMINOFACIEN (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.42 Å
AuthorsHarms, J.M. / Schluenzen, F. / Fucini, P. / Bartels, H. / Yonath, A.
CitationJournal: Bmc Biol. / Year: 2004
Title: Alterations at the Peptidyl Transferase Centre of the Ribosome Induced by the Synergistic Action of the Streptogramins Dalfopristin and Quinupristin.
Authors: Harms, J.M. / Schlunzen, F. / Fucini, P. / Bartels, H. / Yonath, A.
History
DepositionMar 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S RIBOSOMAL RNA
1: 50S RIBOSOMAL PROTEIN L33
2: 50S RIBOSOMAL PROTEIN L34
3: 50S RIBOSOMAL PROTEIN L35
4: 50S RIBOSOMAL PROTEIN L36
5: QUINUPRISTIN
9: 5S RIBOSOMAL RNA
A: 50S RIBOSOMAL PROTEIN L2
B: 50S RIBOSOMAL PROTEIN L3
C: 50S RIBOSOMAL PROTEIN L4
D: 50S RIBOSOMAL PROTEIN L5
E: 50S RIBOSOMAL PROTEIN L6
F: 50S RIBOSOMAL PROTEIN L9
G: 50S RIBOSOMAL PROTEIN L11
H: 50S RIBOSOMAL PROTEIN L13
I: 50S RIBOSOMAL PROTEIN L14
J: 50S RIBOSOMAL PROTEIN L15
K: 50S RIBOSOMAL PROTEIN L16
L: 50S RIBOSOMAL PROTEIN L17
M: 50S RIBOSOMAL PROTEIN L18
N: 50S RIBOSOMAL PROTEIN L19
O: 50S RIBOSOMAL PROTEIN L20
P: 50S RIBOSOMAL PROTEIN L21
Q: 50S RIBOSOMAL PROTEIN L22
R: 50S RIBOSOMAL PROTEIN L23
S: 50S RIBOSOMAL PROTEIN L24
T: GENERAL STRESS PROTEIN CTC
U: 50S RIBOSOMAL PROTEIN L27
W: 50S RIBOSOMAL PROTEIN L29
X: 50S RIBOSOMAL PROTEIN L30
Y: 50S RIBOSOMAL PROTEIN L31
Z: 50S RIBOSOMAL PROTEIN L32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,390,05933
Polymers1,389,36832
Non-polymers6911
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.500, 406.000, 693.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: 6460405
#7: RNA chain 5S RIBOSOMAL RNA /


Mass: 39911.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: 6460405

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50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules 1234ABCDEFGHIJKLMNOPQRSUWXYZ

#2: Protein 50S RIBOSOMAL PROTEIN L33 / / Coordinate model: Cα atoms only


Mass: 9294.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSS4
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L34 / / Coordinate model: Cα atoms only


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSH2
#4: Protein 50S RIBOSOMAL PROTEIN L35 / / Coordinate model: Cα atoms only


Mass: 7448.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSW6
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / / Coordinate model: Cα atoms only


Mass: 4322.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSK0
#8: Protein 50S RIBOSOMAL PROTEIN L2 / / Coordinate model: Cα atoms only


Mass: 30107.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ9
#9: Protein 50S RIBOSOMAL PROTEIN L3 / / Coordinate model: Cα atoms only


Mass: 22477.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXK2
#10: Protein 50S RIBOSOMAL PROTEIN L4 / / Coordinate model: Cα atoms only


Mass: 22308.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXK1
#11: Protein 50S RIBOSOMAL PROTEIN L5 / / Coordinate model: Cα atoms only


Mass: 20379.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ0
#12: Protein 50S RIBOSOMAL PROTEIN L6 / / Coordinate model: Cα atoms only


Mass: 22867.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSL3
#13: Protein 50S RIBOSOMAL PROTEIN L9 / / Coordinate model: Cα atoms only


Mass: 16089.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RY49
#14: Protein 50S RIBOSOMAL PROTEIN L11 / / Coordinate model: Cα atoms only


Mass: 14889.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSS7
#15: Protein 50S RIBOSOMAL PROTEIN L13 / / Coordinate model: Cα atoms only


Mass: 19223.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXY1
#16: Protein 50S RIBOSOMAL PROTEIN L14 / / Coordinate model: Cα atoms only


Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ2
#17: Protein 50S RIBOSOMAL PROTEIN L15 / / Coordinate model: Cα atoms only


Mass: 16894.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSK9
#18: Protein 50S RIBOSOMAL PROTEIN L16 / / Coordinate model: Cα atoms only


Mass: 16257.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ5
#19: Protein 50S RIBOSOMAL PROTEIN L17 / / Coordinate model: Cα atoms only


Mass: 12926.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSJ5
#20: Protein 50S RIBOSOMAL PROTEIN L18 / / Coordinate model: Cα atoms only


Mass: 12163.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSL2
#21: Protein 50S RIBOSOMAL PROTEIN L19 / / Coordinate model: Cα atoms only


Mass: 18347.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RWB4
#22: Protein 50S RIBOSOMAL PROTEIN L20 / / Coordinate model: Cα atoms only


Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSW7
#23: Protein 50S RIBOSOMAL PROTEIN L21 / / Coordinate model: Cα atoms only


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RY64
#24: Protein 50S RIBOSOMAL PROTEIN L22 / / Coordinate model: Cα atoms only


Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ7
#25: Protein 50S RIBOSOMAL PROTEIN L23 / / Coordinate model: Cα atoms only


Mass: 10539.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXK0
#26: Protein 50S RIBOSOMAL PROTEIN L24 / / Coordinate model: Cα atoms only


Mass: 12384.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ1
#28: Protein 50S RIBOSOMAL PROTEIN L27 / / Coordinate model: Cα atoms only


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RY65
#29: Protein 50S RIBOSOMAL PROTEIN L29 / / Coordinate model: Cα atoms only


Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ4
#30: Protein 50S RIBOSOMAL PROTEIN L30 / / Coordinate model: Cα atoms only


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSL0
#31: Protein 50S RIBOSOMAL PROTEIN L31 / / Coordinate model: Cα atoms only


Mass: 8597.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RW44
#32: Protein 50S RIBOSOMAL PROTEIN L32 / / Coordinate model: Cα atoms only


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: P49228

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Protein/peptide / Protein / Non-polymers , 3 types, 3 molecules 5T

#27: Protein GENERAL STRESS PROTEIN CTC / Coordinate model: Cα atoms only


Mass: 27004.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RX88
#33: Chemical ChemComp-DOL / 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE / DALFOPRISTIN / Dalfopristin


Mass: 690.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50N4O9S / Comment: antibiotic*YM
#6: Protein/peptide QUINUPRISTIN / / PRISTINAMYCIN IA / RP 57669 /


Type: Oligopeptide / Class: Antibiotic / Mass: 1024.236 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: QUINUPRISTIN IS A CYLIC HEPTAPEPTIDE. THE RING GENERATED BY LINKING RESIDUE 2 SIDE-CHAIN IS AND MAIN-CHAIN RESIDUE 7.
Source: (synth.) STREPTOMYCES GRAMINOFACIEN (bacteria) / References: Quinupristin

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Details

Compound detailsQUINUPRISTIN IS A STREPTOGRAMIN ANTIBIOTIC. HERE, QUINUPRISTIN IS REPRESENTED BY SEQUENCE (SEQRES).

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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: 4.27 Å3/Da / Density % sol: 64 %
Crystal growpH: 7.8
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ethanol11
2DIMETHYLHEXANEDIOL11
3KCl11
4MgCl211
5NH4Cl11
6HEPES11
7H2O11
8MgCl212
9NH4Cl12
10H2O12

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: SBC / Detector: CCD / Date: Nov 14, 2001
RadiationMonochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.42→30 Å / Num. obs: 282979 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Rsym value: 0.16 / Net I/σ(I): 11.5
Reflection shellResolution: 3.42→3.54 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.4 / % possible all: 81.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1LNR

1lnr
PDB Unreleased entry


Resolution: 3.42→15 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.348 14131 5 %RANDOM
Rwork0.278 ---
obs0.278 266331 --
Refinement stepCycle: LAST / Resolution: 3.42→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 61875 48 0 65418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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