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- PDB-3cqz: Crystal structure of 10 subunit RNA polymerase II in complex with... -

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Basic information

Entry
Database: PDB / ID: 3cqz
TitleCrystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...) x 5
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...) x 5
  • ALPHA-AMANITIN
KeywordsTRANSCRIPTION/TOXIN / TRANSCRIPTION-TOXIN COMPLEX / ALPHA AMANITIN / TOXIN / INHIBITOR / POLYMERASE / TRANSFERASE / DNA BINDING / ZINC-FINGER / PHOSPHOPROTEIN / TRANSCRIPTION
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / toxin activity / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
RNA polymerase II, clamp domain / DNA Excision Repair, Uvrb; Chain A / Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Enzyme I; Chain A, domain 2 ...RNA polymerase II, clamp domain / DNA Excision Repair, Uvrb; Chain A / Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Enzyme I; Chain A, domain 2 / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / 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 Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, 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, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Gyrase A; domain 2 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / Homeodomain-like / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6
Similarity search - Domain/homology
Alpha-Amanitin / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 ...Alpha-Amanitin / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Alpha-amanitin proprotein
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
AMANITA PHALLOIDES (death cap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKaplan, C.D. / Larsson, K.-M. / Kornberg, R.D.
CitationJournal: Mol.Cell / Year: 2008
Title: The RNA Polymerase II Trigger Loop Functions in Substrate Selection and is Directly Targeted by Alpha-Amanitin.
Authors: Kaplan, C.D. / Larsson, K.M. / Kornberg, R.D.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: 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: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Aug 30, 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_conn_type / struct_sheet
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BO" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
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
M: ALPHA-AMANITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,08819
Polymers470,56511
Non-polymers5238
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52250 Å2
ΔGint-259.2 kcal/mol
Surface area138660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.510, 222.480, 374.230
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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DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 5 types, 5 molecules ABCIK

#1: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / RNA POLYMERASE II SUBUNIT B1 / RNA POLYMERASE II SUBUNIT 1 / DNA-DIRECTED RNA POLYMERASE III ...RNA POLYMERASE II SUBUNIT B1 / RNA POLYMERASE II SUBUNIT 1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / RNA POLYMERASE II SUBUNIT 2 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE / B150


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / RNA POLYMERASE II SUBUNIT B3 / RNA POLYMERASE II SUBUNIT 3 / DNA-DIRECTED RNA POLYMERASE II 45 KDA ...RNA POLYMERASE II SUBUNIT B3 / RNA POLYMERASE II SUBUNIT 3 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / B44.5


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16370
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / RNA POLYMERASE II SUBUNIT B9 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 / DNA-DIRECTED RNA ...RNA POLYMERASE II SUBUNIT B9 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / B12.6


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P27999
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / RNA POLYMERASE II SUBUNIT B11 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE / B13.6


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

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ... , 5 types, 5 molecules EFHJL

#4: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 27 ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / ABC27


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20434
#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 23 ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / ABC23


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 14.5 ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE / ABC14.5 / ABC14.4


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20436
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 8.3 ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / DNA- DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTIDE / ABC10-BETA / ABC8


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 / 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 (brewer's yeast) / References: UniProt: P40422

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Protein/peptide , 1 types, 1 molecules M

#11: Protein/peptide ALPHA-AMANITIN / AMATOXIN / ALPHA AMANITIN


Type: Cyclic peptide / Class: Toxin / Mass: 939.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ALPHA-AMANITIN, IS AN 8 AMINO-ACID PEPTIDE. THE OUTER LOOP IS FORMED BY A PEPTIDE BOND BETWEEN THE C- AND THE N-TERMINI. THE SIDE-CHAINS OF RESIDUES 2 AND 8 ARE LINKED TO FORM THE INNER LOOP.
Source: (synth.) AMANITA PHALLOIDES (death cap) / References: UniProt: P85421, Alpha-Amanitin

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Non-polymers , 2 types, 25 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsALPHA-AMANITIN, AN AMATOXIN, IS A DI-CYCLIC PEPTIDE. HERE, ALPHA-AMANITIN IS REPRESENTED BY THE ...ALPHA-AMANITIN, AN AMATOXIN, IS A DI-CYCLIC PEPTIDE. HERE, ALPHA-AMANITIN IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.6 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 124441

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K83

1k83


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.878 / SU B: 31.53 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.598 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3507 3 %RANDOM
Rwork0.2 ---
obs0.202 112956 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27315 0 8 17 27340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02227820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.97137574
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.94253397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21424.0861285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.707155063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.03615206
X-RAY DIFFRACTIONr_chiral_restr0.1390.24231
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220793
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2560.213213
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.218882
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2887
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.517495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.393227678
X-RAY DIFFRACTIONr_scbond_it1.783311454
X-RAY DIFFRACTIONr_scangle_it2.9844.59896
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 233 -
Rwork0.312 7105 -
obs--81.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.40021.1734-0.82772.5307-1.59851.4609-0.06110.35520.0427-0.30140.25880.41650.3347-0.3098-0.19770.00010-0.000100034.68142.24161.555
20.68690.22260.21130.58010.24481.1780.0148-0.1140.02820.1545-0.00130.0638-0.1669-0.1201-0.0135-0.03920.060.0625-0.213-0.0237-0.106173.31667.24874.005
30.4808-0.27680.07970.7219-0.18610.60730.13180.1608-0.0391-0.169-0.0998-0.0926-0.03870.1581-0.0319-0.2168-0.02740.064-0.0255-0.0869-0.150993.59740.1832.386
40.79350.04750.92061.77740.56191.3869-0.0152-0.0054-0.06890.42730.07570.0221-0.0075-0.1046-0.0604-0.0039-0.07310.027-0.00260.0640.036687.92511.76191.411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 154
2X-RAY DIFFRACTION1A161 - 186
3X-RAY DIFFRACTION1A199 - 346
4X-RAY DIFFRACTION1A1398 - 1445
5X-RAY DIFFRACTION1B1151 - 1222
6X-RAY DIFFRACTION2A809 - 1141
7X-RAY DIFFRACTION2A1275 - 1388
8X-RAY DIFFRACTION2E3 - 215
9X-RAY DIFFRACTION2F72 - 155
10X-RAY DIFFRACTION3A347 - 808
11X-RAY DIFFRACTION3B20 - 69
12X-RAY DIFFRACTION3B90 - 217
13X-RAY DIFFRACTION3C3 - 267
14X-RAY DIFFRACTION3B406 - 430
15X-RAY DIFFRACTION3B446 - 668
16X-RAY DIFFRACTION3B678 - 712
17X-RAY DIFFRACTION3B722 - 917
18X-RAY DIFFRACTION3B933 - 1150
19X-RAY DIFFRACTION3J1 - 65
20X-RAY DIFFRACTION3K2 - 114
21X-RAY DIFFRACTION3L26 - 70
22X-RAY DIFFRACTION3H2 - 61
23X-RAY DIFFRACTION3H76 - 146
24X-RAY DIFFRACTION3I40 - 120
25X-RAY DIFFRACTION4A1142 - 1176
26X-RAY DIFFRACTION4A1187 - 1272
27X-RAY DIFFRACTION4B218 - 335
28X-RAY DIFFRACTION4B345 - 405
29X-RAY DIFFRACTION4I2 - 39

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