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- PDB-3tgu: Cytochrome bc1 complex from chicken with pfvs-designed moa inhibi... -

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Basic information

Entry
Database: PDB / ID: 3tgu
TitleCytochrome bc1 complex from chicken with pfvs-designed moa inhibitor bound
Components
  • (Cytochrome b-c1 complex subunit Rieske, ...) x 2
  • (Mitochondrial ubiquinol-cytochrome c reductase ...) x 4
  • (Mitochondrial ubiquinol-cytochrome-c reductase complex core protein ...) x 2
  • Cytochrome b
  • Mitochondrial cytochrome c1, heme protein
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEIN / UBIQUINONE / OXIDOREDUCTASE / REDOX ENZYME / RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE / MEMBRANE / STROBILURINS BINDING / MITOCHONDRION / TRANSMEMBRANE / IRON / MITOCHONDRIAL INNER MEMBRANE / IRON-SULFUR / TRANSIT PEPTIDE / METAL-BINDING / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / electron transfer activity ...Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / electron transfer activity / oxidoreductase activity / heme binding / mitochondrion / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C ...Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Unknown ligand / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Chem-WF3 / Mitochondrial cytochrome c1, heme protein / Complex III subunit 9 ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Unknown ligand / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Chem-WF3 / Mitochondrial cytochrome c1, heme protein / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2 / Cytochrome b-c1 complex subunit 7 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i / Cytochrome b-c1 complex subunit 8 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuang, L.-S. / Yang, G.-F. / Berry, E.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex.
Authors: Hao, G.F. / Wang, F. / Li, H. / Zhu, X.L. / Yang, W.C. / Huang, L.S. / Wu, J.W. / Berry, E.A. / Yang, G.F.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Sep 13, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_poly / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i
B: Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2
C: Cytochrome b
D: Mitochondrial cytochrome c1, heme protein
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein
G: Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
H: Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein
N: Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i
O: Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2
P: Cytochrome b
Q: Mitochondrial cytochrome c1, heme protein
R: Cytochrome b-c1 complex subunit Rieske, mitochondrial
S: Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein
T: Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
U: Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii
V: Cytochrome b-c1 complex subunit Rieske, mitochondrial
W: Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,60451
Polymers467,99220
Non-polymers18,61231
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area103730 Å2
ΔGint-709 kcal/mol
Surface area155020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.678, 183.305, 241.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Mitochondrial ubiquinol-cytochrome-c reductase complex core protein ... , 2 types, 4 molecules ANBO

#1: Protein Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i / UQCRC1


Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX31, quinol-cytochrome-c reductase
#2: Protein Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2 / UQCRC2


Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX29, quinol-cytochrome-c reductase

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Protein , 2 types, 4 molecules CPDQ

#3: Protein Cytochrome b / / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42650.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P18946
#4: Protein Mitochondrial cytochrome c1, heme protein


Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX26, quinol-cytochrome-c reductase

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Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules ERIV

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron- ...Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 77-272 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase
#9: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron- ...Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 7721.072 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-8; UNP RESIDUES 48-76 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase

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Mitochondrial ubiquinol-cytochrome c reductase ... , 4 types, 8 molecules FSGTHUJW

#6: Protein Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein / UQCRB


Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX30, quinol-cytochrome-c reductase
#7: Protein Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c / UQCRQ


Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX32, quinol-cytochrome-c reductase
#8: Protein Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii / UQCRH / HINGE PROTEIN


Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX28, quinol-cytochrome-c reductase
#10: Protein Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein / UQCR10


Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX27, quinol-cytochrome-c reductase

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Sugars , 1 types, 5 molecules

#19: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 10 types, 47 molecules

#11: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#12: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-WF3 / methyl (2E)-3-methoxy-2-[2-({[6-methyl-3-(trifluoromethyl)quinoxalin-2-yl]oxy}methyl)phenyl]prop-2-enoate


Mass: 432.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19F3N2O4
#14: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#15: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#17: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#18: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#21: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsANOTHER SUBUNIT OF THE BIOLOGICAL ASSEMBLY (SUBUNIT 11) IS LOST DURING PURIFICATION OR ...ANOTHER SUBUNIT OF THE BIOLOGICAL ASSEMBLY (SUBUNIT 11) IS LOST DURING PURIFICATION OR CRYSTALLIZATION AND IS NOT PRESENT IN THE DEPOSITED STRUCTURE
Sequence detailsTHOUGH THE CRYSTALLIZED SEQUENCE CORRESPONDING TO CHAIN I AND V WAS PROBABLY NOT CLEAVED BY ...THOUGH THE CRYSTALLIZED SEQUENCE CORRESPONDING TO CHAIN I AND V WAS PROBABLY NOT CLEAVED BY PROTEOLYSIS, THE COORDINATES MODEL CONTAIN A SEGMENT CORRESPONDING TO POLY UNK WITH UNKNOWN SEQUENCE AND CONNECTIVITY. PERHAPS, THE SEQUENCE FOR THE POLY UNK SHOULD BE: KALAPAALRAEKVVL

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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: 4.09 Å3/Da / Density % sol: 69.93 %
Crystal growTemperature: 278 K / pH: 6.77
Details: 50 mm cacodylate, 9.4 mM TrisHCl, 30 mM K-MES, 1.8 mM K-MOPS, 30 mM NaCl, 31 mM KCl, 10 mM MgCl2, 91 g/l glycerol, 30 g/l PEG 4kDa, 0.9 mM NaN3, 0.05 mM EDTA, 0.47g/l undecyl maltoside, 31 ...Details: 50 mm cacodylate, 9.4 mM TrisHCl, 30 mM K-MES, 1.8 mM K-MOPS, 30 mM NaCl, 31 mM KCl, 10 mM MgCl2, 91 g/l glycerol, 30 g/l PEG 4kDa, 0.9 mM NaN3, 0.05 mM EDTA, 0.47g/l undecyl maltoside, 31 mM octyl glucoside, pH 6.77, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 6, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 192851 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 73 Å2 / Rsym value: 0.103 / Net I/σ(I): 10.97
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 0.98 / Rsym value: 0.779 / % possible all: 55.2

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Processing

Software
NameClassification
Adxvdata processing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L71

3l71


Resolution: 2.7→24.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4290036.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3737 2 %RANDOM
Rwork0.258 ---
obs0.258 191170 91.1 %-
all-191170 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.47 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 78.7 Å2
Baniso -1Baniso -2Baniso -3
1-39.26 Å20 Å20 Å2
2---20.39 Å20 Å2
3----18.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31867 0 845 21 32733
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.442
X-RAY DIFFRACTIONc_mcangle_it3.973
X-RAY DIFFRACTIONc_scbond_it6.54.5
X-RAY DIFFRACTIONc_scangle_it8.76
LS refinement shellResolution: 2.7→2.84 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.404 349 1.9 %
Rwork0.4 17752 -
obs--61 %

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