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- PDB-8abk: Complex III2 from Yarrowia lipolytica, decylubiquinol bound, b-po... -

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Basic information

Entry
Database: PDB / ID: 8abk
TitleComplex III2 from Yarrowia lipolytica, decylubiquinol bound, b-position
Components
  • (Cytochrome b-c1 complex subunit ...) x 4
  • Complex III subunit 9
  • Cytochrome b
  • YALI0A14806p
  • YALI0A17468p
  • YALI0C12210p
  • YALI0F24673p
KeywordsMEMBRANE PROTEIN / oxidoreductase / electron transport chain
Function / homology
Function and homology information


mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista ...mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / nuclear periphery / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 ...Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / 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 / : / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / Chem-DCQ / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / YALI0F24673p / Cytochrome b-c1 complex subunit 2, mitochondrial ...CARDIOLIPIN / Chem-DCQ / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / YALI0F24673p / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 7 / YALI0C12210p / Complex III subunit 9 / quinol--cytochrome-c reductase / mitochondrial processing peptidase / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWieferig, J.P. / Kuhlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: IUCrJ / Year: 2023
Title: Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III by cryo-EM.
Authors: Jan Philip Wieferig / Werner Kühlbrandt /
Abstract: Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain ...Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII with a reduced high-potential chain increased the occupancy of the Q site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification ..._em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cytochrome b
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
G: Cytochrome b-c1 complex subunit 7
F: YALI0F24673p
A: YALI0A14806p
B: Cytochrome b-c1 complex subunit 2, mitochondrial
D: YALI0A17468p
H: Cytochrome b-c1 complex subunit 8
I: Complex III subunit 9
J: YALI0C12210p
N: Cytochrome b
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
R: Cytochrome b-c1 complex subunit 7
Q: YALI0F24673p
L: YALI0A14806p
M: Cytochrome b-c1 complex subunit 2, mitochondrial
O: YALI0A17468p
S: Cytochrome b-c1 complex subunit 8
T: Complex III subunit 9
U: YALI0C12210p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,95953
Polymers519,47220
Non-polymers28,48733
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21N
12P
22E
13G
23R
14F
24Q
15A
25L
16B
26M
17D
27O
18H
28S
19I
29T
110J
210U

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUCA1 - 3831 - 383
21METMETLEULEUNK1 - 3831 - 383
12GLYGLYASPASPPB39 - 9639 - 96
22GLYGLYASPASPEL39 - 9639 - 96
13ALAALAVALVALGC2 - 1252 - 125
23ALAALAVALVALRM2 - 1252 - 125
14PROPROLEULEUFD76 - 14666 - 136
24PROPROLEULEUQN76 - 14666 - 136
15VALVALTRPTRPAE26 - 47426 - 474
25VALVALTRPTRPLO26 - 47426 - 474
16PHEPHELEULEUBF15 - 41615 - 416
26PHEPHELEULEUMP15 - 41615 - 416
17METMETPROPRODG85 - 32885 - 328
27METMETPROPROOQ85 - 32885 - 328
18TYRTYRLEULEUHH9 - 937 - 91
28TYRTYRLEULEUSR9 - 937 - 91
19ALAALATYRTYRII4 - 574 - 57
29ALAALATYRTYRTS4 - 574 - 57
110TYRTYRPHEPHEJJ8 - 828 - 82
210TYRTYRPHEPHEUT8 - 828 - 82

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 6 types, 12 molecules CNFQALDOITJU

#1: 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: 43409.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q9B6D0
#4: Protein YALI0F24673p


Mass: 15789.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C0H4
#5: Protein YALI0A14806p


Mass: 52846.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CGY9
#7: Protein YALI0A17468p


Mass: 36555.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CGP7
#9: Protein Complex III subunit 9


Mass: 8038.856 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CG23
#10: Protein YALI0C12210p


Mass: 9114.678 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CC60

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Cytochrome b-c1 complex subunit ... , 4 types, 8 molecules PEGRBMHS

#2: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 24563.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CI02, quinol-cytochrome-c reductase
#3: Protein Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 14675.995 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C3K7
#6: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 44277.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C2E3
#8: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII


Mass: 10463.970 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C387

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Sugars , 1 types, 4 molecules

#16: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 29 molecules

#11: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#13: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#14: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#15: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30O4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-XP4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 591.777 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H60O8P / Comment: DMPA, phospholipid*YM
#19: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex III2, with decylubiquinol, b-position / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0258 / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10REFMACmodel refinement
11RELIONinitial Euler assignment
12RELIONfinal Euler assignment
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69259 / Symmetry type: POINT
RefinementHighest resolution: 2.5 Å
Refinement stepCycle: 1 / Total: 32573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01233404
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.6671.66145399
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.6653974
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.45522.2441600
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.468155138
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.0415166
ELECTRON MICROSCOPYr_chiral_restr0.1070.24330
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0225176
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.8766.28215965
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it4.7829.43219916
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it4.346.77717439
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined13.32613.326140207
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C269980.04
12N269980.04
21P33240.07
22E33240.07
31G82920.06
32R82920.06
41F45860.08
42Q45860.08
51A293580.07
52L293580.07
61B256180.09
62M256180.09
71D158540.03
72O158540.03
81H51960.01
82S51960.01
91I37080.01
92T37080.01
101J45420.06
102U45420.06
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.616 24048 -
obs--100 %

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