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- PDB-2ja5: CPD lesion containing RNA Polymerase II elongation complex A -

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Basic information

Entry
Database: PDB / ID: 2ja5
TitleCPD lesion containing RNA Polymerase II elongation complex A
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TTP*TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'
  • 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'
KeywordsTRANSFERASE / DNA-DIRECTED RNA POLYMERASE / LESION RECOGNITION / TRANSFERASE/DNA/RNA / DNA DAMAGE / ZINC-FINGER / DNA-BINDING / PHOTOLESION / PHOSPHORYLATION / MISINCORPORATION / RNA POLYMERASE II / TRANSCRIPTION- COUPLED REPAIR / CYCLOBUTANE PYRIMIDINE DIMER / TCR / CPD / ZINC / ARREST / STALLING / DNA LESION / METAL-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION BUBBLE / NUCLEOTIDYLTRANSFERASE / DAMAGE RECOGNITION / ELONGATION COMPLEX / THYMINE DIMER / TRANSCRIPTION
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE ...nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / positive regulation of translational initiation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation from RNA polymerase II promoter / translation initiation factor binding / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 ...Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Enzyme I; Chain A, domain 2 / RNA polymerase, Rpb5, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 6 / Eukaryotic RNA polymerase II heptapeptide repeat. / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase Rpb4 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / RNA polymerase Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RNA polymerase Rpb5, C-terminal domain / RPB5-like RNA polymerase subunit superfamily / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / C2C2 Zinc finger / Zinc finger, TFIIS-type / Gyrase A; domain 2
Similarity search - Domain/homology
RNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA ...RNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / DNA / DNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsBrueckner, F. / Hennecke, U. / Carell, T. / Cramer, P.
CitationJournal: Science / Year: 2007
Title: Cpd Damage Recognition by Transcribing RNA Polymerase II
Authors: Brueckner, F. / Hennecke, U. / Carell, T. / Cramer, P.
History
DepositionNov 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Derived calculations / Version format compliance
Revision 1.2Sep 16, 2015Group: Source and taxonomy
Revision 1.3Mar 29, 2017Group: Database references
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
P: 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'
T: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TTP*TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,14623
Polymers525,59814
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)222.209, 392.206, 284.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P16370
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P20433
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P34087
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P27999
#11: Protein DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P20434
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P20435
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20436
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22139
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40422

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RNA chain / DNA chain , 2 types, 2 molecules PT

#13: RNA chain 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' / PRODUCT RNA OF COMPLEX A


Mass: 3506.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#14: DNA chain 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TTP*TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' / THYMINE-THYMINE CPD CONTAINING TEMPLATE DNA OF COMPLEX A


Mass: 7934.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 9 molecules

#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 6.98 Å3/Da / Density % sol: 82.24 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9191
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 120477 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y1W
Resolution: 3.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 4590 1.9 %RANDOM
Rwork0.2701 ---
obs0.2701 230113 97.4 %-
Solvent computationBsol: 111.095 Å2 / ksol: 0.406571 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.625 Å20 Å20 Å2
2--25.533 Å20 Å2
3----42.157 Å2
Refinement stepCycle: LAST / Resolution: 3.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31220 431 9 0 31660
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.55
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
LS refinement shellResolution: 3.8→3.83 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3595 76 1.9 %
Rwork0.3762 3809 -

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