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- PDB-8ab6: Complex III2 from Yarrowia lipolytica, combined datasets, consens... -

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Basic information

Entry
Database: PDB / ID: 8ab6
TitleComplex III2 from Yarrowia lipolytica, combined datasets, consensus refinement
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 / ubiquinol-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 / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / nuclear periphery / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
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 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 / 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 ...CARDIOLIPIN / 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 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 1.2Nov 13, 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)547,13850
Polymers519,47220
Non-polymers27,66630
Water23,8881326
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: 1 / Refine code: 1

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
12GLYGLYALAALAPB39 - 10139 - 101
22GLYGLYALAALAEL39 - 10139 - 101
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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, 9.0E-6, -3.6E-5), (-9.0E-6, -1, 5.2E-5), (-3.6E-5, 5.2E-5, 1)118.85619, 130.56802, -0.00196

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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

#15: 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 , 7 types, 1352 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
#16: 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
#17: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1326 / Source method: isolated from a natural source / Formula: H2O

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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, consensus refinement of combined datasets
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 R2/2
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
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
14REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1419666 / Symmetry type: POINT
RefinementResolution: 2→162.38 Å / Cor.coef. Fo:Fc: 0.82 / SU B: 5.337 / SU ML: 0.13 / ESU R: 0.139
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.27319 --
obs0.27319 637921 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 30.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.18 Å20 Å2
2--0.03 Å20 Å2
3----0.84 Å2
Refinement stepCycle: 1 / Total: 32925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01232396
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.5311.66144038
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.51253860
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.05122.361534
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.945154980
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.20115158
ELECTRON MICROSCOPYr_chiral_restr0.1020.24208
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0224382
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_it1.2492.95115494
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it2.2484.42619330
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.7093.19716902
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined7.8555.018137362
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: C / Refine-ID: ELECTRON MICROSCOPY

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
1010598tight positional0.070.05
113055tight thermal0.140.5
22478tight thermal0.360.5
33994tight thermal0.190.5
44579tight thermal0.340.5
553446tight thermal0.340.5
663008tight thermal0.30.5
771893tight thermal0.210.5
88690tight thermal0.030.5
99452tight thermal0.030.5
1010598tight thermal0.150.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.512 47181 -
obs--100 %

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