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- PDB-4x6z: Yeast 20S proteasome in complex with PR-VI modulator -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4x6z
TitleYeast 20S proteasome in complex with PR-VI modulator
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
  • synthetic peptide (polymer)
KeywordsHYDROLASE / 20S proteasome / low-molecular mass activators / allosteric regulation
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRostankowski, R. / Witkowska, J. / Borek, D. / Otwinowski, Z. / Jankowska, E.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science CentreNCN 2011/01/B/ST5/06616 Poland
CitationJournal: To Be Published
Title: Crystal structures revealed the common place of binding of low-molecular mass activators with the 20S proteasome
Authors: Witkowska, J. / Rostankowski, R. / Dubin, G. / Grudnik, P. / Golik, P. / Gaczynska, M. / Osmulski, P. / Borek, D. / Otwinowski, Z. / Jankowska, E.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
1: Proteasome subunit beta type-6
2: Proteasome subunit beta type-7
A: Proteasome subunit alpha type-1
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-3
D: Proteasome subunit alpha type-4
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-6
G: Probable proteasome subunit alpha type-7
H: Proteasome subunit beta type-1
I: Proteasome subunit beta type-2
J: Proteasome subunit beta type-3
K: Proteasome subunit beta type-4
L: Proteasome subunit beta type-5
M: Proteasome subunit beta type-6
N: Proteasome subunit beta type-7
O: Proteasome subunit alpha type-1
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-3
R: Proteasome subunit alpha type-4
S: Proteasome subunit alpha type-5
T: Proteasome subunit alpha type-6
U: Probable proteasome subunit alpha type-7
V: Proteasome subunit beta type-1
W: Proteasome subunit beta type-2
X: Proteasome subunit beta type-3
Y: Proteasome subunit beta type-4
Z: Proteasome subunit beta type-5
a: synthetic peptide (polymer)
e: synthetic peptide (polymer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)776,078133
Polymers770,15430
Non-polymers5,924103
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area136650 Å2
ΔGint-821 kcal/mol
Surface area211550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.350, 300.790, 144.580
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
111
21M
122
22N
13A
23O
14B
24P
15C
25Q
16D
26R
17E
27S
18F
28T
19G
29U
110H
210V
111I
211W
112J
212X
113K
213Y
114L
214Z

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASP1A-8 - 21320 - 241
21GLNGLNASPASPMO-8 - 21320 - 241
12THRTHRILEILE2B-7 - 22534 - 266
22THRTHRILEILENP-7 - 22534 - 266
13GLYGLYGLUGLUAC11 - 25011 - 250
23GLYGLYGLUGLUOQ11 - 25011 - 250
14THRTHRGLUGLUBD2 - 2482 - 248
24THRTHRGLUGLUPR2 - 2482 - 248
15GLYGLYTHRTHRCE2 - 2452 - 245
25GLYGLYTHRTHRQS2 - 2452 - 245
16GLYGLYGLNGLNDF3 - 2433 - 243
26GLYGLYGLNGLNRT3 - 2433 - 243
17ASPASPGLUGLUEG9 - 2509 - 250
27ASPASPGLUGLUSU9 - 2509 - 250
18ARGARGILEILEFH3 - 2343 - 234
28ARGARGILEILETV3 - 2343 - 234
19GLYGLYASNASNGI4 - 2475 - 248
29GLYGLYASNASNUW4 - 2475 - 248
110THRTHRLEULEUHJ1 - 19620 - 215
210THRTHRLEULEUVX1 - 19620 - 215
111THRTHRASNASNIK1 - 21930 - 248
211THRTHRASNASNWY1 - 21930 - 248
112SERSERASPASPJL-7 - 1962 - 205
212SERSERASPASPXZ-7 - 1962 - 205
113METMETGLNGLNKM0 - 1951 - 196
213METMETGLNGLNYAA0 - 1951 - 196
114THRTHRGLYGLYLN1 - 21276 - 287
214THRTHRGLYGLYZBA1 - 21276 - 287

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules 1M2NHVIWJXKYLZ

#1: Protein Proteasome subunit beta type-6 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#2: Protein Proteasome subunit beta type-7 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-1 / PSMB1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 23573.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-2 / PSMB2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 28299.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-3 / PSMB3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / PSMB4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-5 / PSMB5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 31670.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P30656, proteasome endopeptidase complex

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Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESFT

#3: Protein Proteasome subunit alpha type-1 / / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-2 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-3 / / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-4 / / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-5 / / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#8: Protein Proteasome subunit alpha type-6 / / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex

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Protein / Protein/peptide , 2 types, 4 molecules GUae

#15: Protein/peptide synthetic peptide (polymer)


Mass: 1673.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex

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Non-polymers , 4 types, 462 molecules

#16: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#17: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C3H8O3
#18: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: Mg
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 30mM magnesium acetate, 12% MPD, 0.1M MES pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→49.46 Å / Num. obs: 207816 / % possible obs: 68.4 % / Redundancy: 1 % / Rsym value: 0.192 / Net I/σ(I): 6.5
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2.9 / % possible all: 20.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
Cootmodel building
MOLREPphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYP

1ryp


Resolution: 2.7→49.46 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.718 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22192 9928 5 %RANDOM
Rwork0.17733 ---
obs0.17957 186914 68.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.523 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å2-1.55 Å2
2--0.42 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49481 0 356 359 50196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01950699
X-RAY DIFFRACTIONr_bond_other_d0.0040.0248553
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.96768524
X-RAY DIFFRACTIONr_angle_other_deg0.983111781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16756343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98424.3742268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.371158784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39715292
X-RAY DIFFRACTIONr_chiral_restr0.0840.27729
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0257362
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0211348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5232.41925426
X-RAY DIFFRACTIONr_mcbond_other1.5232.41925425
X-RAY DIFFRACTIONr_mcangle_it2.5653.62231736
X-RAY DIFFRACTIONr_mcangle_other2.5653.62231737
X-RAY DIFFRACTIONr_scbond_it2.0132.70125273
X-RAY DIFFRACTIONr_scbond_other2.0122.70125273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3533.9436784
X-RAY DIFFRACTIONr_long_range_B_refined6.01923.042209795
X-RAY DIFFRACTIONr_long_range_B_other6.01723.041209751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
111131820.08
12M131820.08
212146470.05
22N146470.05
31A146960.09
32O146960.09
41B146220.07
42P146220.07
51C144320.1
52Q144320.1
61D143010.11
62R143010.11
71E141040.1
72S141040.1
81F136840.1
82T136840.1
91G144260.09
92U144260.09
101H118010.06
102V118010.06
111I126880.08
112W126880.08
121J125120.06
122X125120.06
131K123610.06
132Y123610.06
141L125880.06
142Z125880.06
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 176 -
Rwork0.292 3070 -
obs--15.25 %
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)
110.56580.0808-4.54232.53640.8353.00270.40570.16470.7975-0.15010.0618-0.2868-0.26050.0831-0.46750.21990.0279-0.02890.10640.03560.156467.8535-11.94728.4371
20.7514-0.08510.060.7530.34831.14830.08140.0428-0.1019-0.1752-0.0178-0.29070.03540.0764-0.06370.09820.04130.07490.054-0.0450.257167.9841-20.162526.0715
32.55371.0121-0.52.145-1.30431.3049-0.10680.2628-0.1367-0.50930.0336-0.57180.53410.32330.07320.29720.1130.09740.3265-0.14010.476479.76741.200912.9803
41.9722-0.8696-1.51815.03241.65053.43880.1509-0.1714-0.05750.0244-0.0257-0.5552-0.09780.5005-0.12520.03390.01090.01190.1784-0.06480.329481.0534-7.36630.9893
51.9371-0.24840.39751.6253-0.31611.0240.0825-0.1954-0.12380.2716-0.0569-0.13760.03870.0017-0.02560.1320.019-0.05530.04630.00980.084155.567-18.50658.0789
60.45770.40190.17691.9725-0.2390.85070.01440.0522-0.08780.09110.0199-0.32330.13750.1108-0.03430.06520.0326-0.03960.0275-0.03870.156862.8654-22.673849.6614
71.7116-0.0635-0.10021.6145-0.10881.1932-0.0581-0.2101-0.08220.23090.0328-0.36860.00360.17380.02530.08940.0089-0.12280.05070.01040.187868.2716-11.256663.4996
82.882-2.63581.63625.6652-0.80281.7846-0.1643-0.1640.3680.47040.1517-0.3458-0.2096-0.04390.01270.2158-0.0713-0.02880.0984-0.05040.171157.686312.031771.1466
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450.54490.40640.35072.18870.51221.28880.0035-0.017-0.0736-0.18960.0191-0.1738-0.00910.1236-0.02260.1167-0.0090.13210.06720.00310.168463.101423.3618.0297
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470.5082-0.0909-0.68160.01820.12130.9264-0.0596-0.2601-0.07670.04050.03770.01330.06330.34690.02190.51930.10480.01170.9334-0.06870.577666.547720.144332.6402
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4912.28845.0486-1.70593.6757-0.66781.49890.1816-0.2372-0.11020.119-0.1161-0.0187-0.10680.0394-0.06550.22720.0374-0.00810.1007-0.01780.120439.568316.6099-2.9736
500.98090.13980.45143.05660.74380.618-0.03810.04250.1469-0.38210.04660.0356-0.05390.0091-0.00860.1743-0.01530.04980.08160.02250.092541.09831.25284.2851
511.6341-0.1668-0.25461.60810.22653.0095-0.01960.03180.1243-0.25530.0663-0.21820.07020.016-0.04670.1661-0.0120.08760.0192-0.00780.061949.949420.00550.6667
520.670.7466-0.11485.3853-0.20770.1721-0.02550.3028-0.0749-0.7050.0320.13180.1297-0.0639-0.00650.2513-0.00770.00920.2466-0.01170.102141.396115.1435-9.746
531.13070.4179-0.40340.72350.50921.23020.01860.03320.0132-0.17690.00650.1778-0.1016-0.0185-0.02510.13760.0398-0.10020.05270.04650.242412.436923.39228.974
543.6411-2.01192.95328.237-7.627811.9287-0.12640.30170.2026-0.1526-0.0066-0.0163-0.46020.05490.1330.214-0.0167-0.03820.13460.0180.210214.650927.4893-0.8953
551.32140.6040.04382.22660.33451.3814-0.03470.1780.0024-0.45870.13450.19140.0106-0.0343-0.09980.17680.0009-0.10110.07310.06110.17429.718513.4523-1.5067
565.95982.0943-1.558310.4368-4.946513.2787-0.07350.5733-0.2934-0.3477-0.07140.43550.0309-0.27930.14490.1474-0.0328-0.08460.1812-0.04220.17-0.5747-3.5356-5.7815
578.8612-0.56862.83612.1493-0.63262.80370.3438-0.0887-0.6003-0.06070.01190.28940.1886-0.154-0.35570.18760.00650.03060.0703-0.02420.1471-0.502312.108431.9065
580.37050.12130.25971.2649-0.35591.15640.0254-0.02160.0635-0.10890.04910.3107-0.0199-0.0719-0.07440.0410.0099-0.00760.01840.04650.2590.620421.313430.8521
592.10030.4211.6941.37981.20153.73430.0045-0.07520.1714-0.244-0.110.4291-0.4016-0.48620.10560.13860.0391-0.08340.14040.09390.3906-11.16481.938214.8564
601.8271-1.2049-0.3974.72040.02112.00360.2217-0.00140.0055-0.2011-0.14470.64980.0929-0.2262-0.07710.0431-0.0192-0.01060.12710.05880.358-12.82167.4733.1393
612.04560.41810.31192.11820.00081.10930.0739-0.210.08390.2698-0.04080.1784-0.1058-0.0756-0.03310.12990.01760.09380.0429-0.0090.093613.843913.40861.5705
620.43980.124-0.2031.34440.13341.00650.0428-0.03370.07020.1511-0.00620.3724-0.0455-0.0911-0.03660.04980.020.07360.02610.01830.20226.785621.021954.0332
632.4012-0.76570.40011.84520.26981.936-0.0039-0.3242-0.06380.27150.05910.41010.0919-0.2764-0.05520.1215-0.02870.16880.12910.01980.27171.15164.963165.0263
645.3479-3.8506-2.04835.8533-1.14683.0197-0.3213-0.2358-0.55890.23540.18910.52310.15640.0680.13220.3541-0.0820.07590.19280.07380.293512.2689-19.463668.7967
651.35670.05580.58011.0895-0.8991.10780.13210.0257-0.13020.0115-0.08060.0050.20510.108-0.05140.34450.0234-0.03810.07050.08420.172427.2621-65.989256.3358
660.3939-0.9863-0.09262.54370.26050.3378-0.0093-0.0336-0.012-0.08050.0638-0.021-0.0359-0.0315-0.05450.1899-0.0186-0.00860.04080.07060.134524.3408-52.332151.5389
670.2329-0.0550.37021.56421.09992.91640.1366-0.1233-0.1190.1829-0.11860.49150.2107-0.2842-0.01810.1897-0.08570.02610.11040.06340.295613.4893-63.283162.7795
683.4006-0.57020.73942.8205-1.37682.71670.0064-0.4029-0.1480.3130.0429-0.11810.0090.1777-0.04930.26010.01880.00010.1070.05370.097122.2584-62.782176.8849
690.3274-0.4353-0.55452.6137-0.19611.6103-0.05160.03-0.21030.0534-0.1490.20470.13740.00190.20060.2456-0.1022-0.07990.09570.00950.303213.0125-65.029730.4576
704.0814-0.92638.72340.23-1.984918.64810.12-0.0577-0.0282-0.0416-0.05990.02840.2848-0.108-0.06010.22170.00220.02370.278-0.00810.34055.3453-64.451152.5969
711.91410.2505-0.211.1102-0.22680.9782-0.03320.0847-0.1649-0.0711-0.00420.3750.1807-0.17020.03740.1347-0.0776-0.07390.05670.00760.23742.1875-56.521233.186
721.21430.95040.19496.46940.13980.9726-0.0084-0.2236-0.17150.1929-0.01170.67580.2023-0.12150.020.1625-0.07540.04690.1980.07160.2989-8.044-55.416346.6569
732.72880.6503-0.49361.10120.23540.61140.1005-0.1225-0.3033-0.22350.0025-0.12290.32880.0606-0.1030.5716-0.0009-0.11270.0441-0.07860.2722.666-65.326411.6115
744.30283.0041-6.66112.6873-3.65112.01060.15670.15960.13130.2155-0.08880.1871-0.0273-0.5931-0.06790.2593-0.0765-0.09730.3305-0.02610.376-1.5652-62.059316.0648
751.40820.03940.05230.5679-0.11140.069-0.01080.0316-0.0839-0.17060.04840.00340.0753-0.0146-0.03760.2084-0.0377-0.09050.0241-0.02880.161314.0644-52.16436.539
761.98890.2382-0.66323.5379-1.43164.49290.05780.20640.09560.06310.07260.6733-0.1592-0.6616-0.13030.237-0.0456-0.16640.2254-0.030.3338-4.8199-59.45341.8185
770.8283-0.33961.53540.90710.1074.06850.16040.0501-0.2207-0.1516-0.01290.01880.35930.0165-0.14740.25860.00060.03090.0872-0.07910.282240.7518-63.28924.6679
786.08260.63090.52960.11760.08690.0688-0.14280.6785-0.11350.06750.10440.04140.06090.04740.03840.658-0.0738-0.01820.4268-0.14770.264222.9467-57.2608-10.6438
791.18410.0095-0.11241.91310.82261.9405-0.01090.1133-0.1617-0.50850.10480.00170.15030.1793-0.09390.3375-0.00260.01430.0623-0.08860.157439.7665-51.0604-6.2401
801.2874-0.10630.34441.71810.50231.34110.14370.5199-0.3421-0.20650.18550.27150.2654-0.2562-0.32920.6043-0.078-0.12890.4593-0.01240.314529.1409-58.4066-23.2481
810.4859-0.09192.00071.7353-0.915711.91960.0019-0.04020.0136-0.0991-0.129-0.02980.39210.34650.1270.25860.06540.04530.1069-0.03640.303155.3866-66.823418.3885
823.3337-0.39991.41681.4096-0.0912.22170.04630.2055-0.1914-0.3116-0.012-0.2977-0.0273-0.0198-0.03430.28860.05430.160.1126-0.09110.237961.6925-53.0989-2.0771
831.85992.413-0.11654.1248-0.27010.81430.03-0.13750.03810.03490.02020.12310.259-0.0845-0.05030.22410.04890.0280.1543-0.06690.206957.9456-44.057415.5831
842.6295-0.1143-0.30450.39910.3631.76660.02320.2259-0.0991-0.26010.0041-0.29640.13240.2061-0.02730.35070.12920.17360.1284-0.06040.347770.5344-56.0197-1.5704
858.45361.9131-7.35570.4335-1.6676.482-0.24280.2792-0.2997-0.0530.0545-0.07460.3218-0.10690.18830.36520.1329-0.07280.261-0.07280.30351.362-70.825436.5598
860.6468-0.4006-0.3691.33791.22182.12250.1528-0.0128-0.2193-0.182-0.1004-0.2650.25170.2015-0.05240.22140.14230.02780.1488-0.00810.473371.1378-50.944932.3178
8713.66484.97721.57799.39870.75853.6053-0.3580.10940.2969-0.24990.10240.33910.0336-0.22780.25560.23640.08890.04870.11290.01760.18356.2959-53.270339.8501
881.27020.0522-0.04680.6783-0.04492.31570.0427-0.0042-0.241-0.03410.0324-0.49860.29310.5339-0.07510.16570.1602-0.01950.1986-0.08310.554680.1767-56.41436.6669
8911.98540.3353-1.87650.4937-0.56470.8537-0.26410.322-0.6732-0.35850.086-0.04160.4041-0.10050.1780.3043-0.0394-0.03220.09320.01090.194338.3704-72.090343.6171
901.83731.1146-0.00621.3309-1.12642.09720.1773-0.1847-0.66410.0392-0.1248-0.38890.34440.1496-0.05260.33670.1394-0.14840.12670.08630.386861.2016-62.386858.7965
911.2660.2706-0.01550.86720.58521.50480.0432-0.1375-0.15430.1180.0278-0.18340.16860.0417-0.0710.20410.0416-0.06090.05020.04710.161348.8163-54.127556.1507
923.9731-1.4959-1.41134.02560.60991.59580.0338-0.4104-0.33060.20670.0732-0.44940.32530.2548-0.1070.25620.0208-0.18580.19190.1130.263763.1992-61.526569.5812
930.7988-0.0309-0.15281.2163-0.18550.53220.062-0.0776-0.08540.1514-0.00290.16840.05120.0011-0.05910.1377-0.02630.01380.03120.03130.065229.5414-25.619762.4411
942.1719-0.5356-0.19163.54760.90231.97220.0586-0.2471-0.16840.36390.0187-0.14570.22530.0474-0.07730.11-0.0346-0.0160.12490.03930.084637.8646-17.67670.5155
951.4251-1.90271.60124.6774-2.41722.5486-0.0594-0.26930.01340.510.01720.0919-0.0887-0.09590.04220.1452-0.0190.06750.16910.01780.045127.1124-15.864276.2466
967.24972.01822.047713.5568-3.69082.14750.0201-0.52290.59130.2123-0.00010.5032-0.2718-0.1351-0.01990.2927-0.01410.09590.2889-0.00150.129518.1201-12.424277.1921
970.5148-0.3328-0.10291.49830.45350.58670.0311-0.0603-0.02590.0891-0.01640.27360.0789-0.0624-0.01460.0953-0.03420.00170.03810.05130.19756.7175-24.154850.4525
980.01740.04650.10675.0945-0.6821.54950.00630.01160.03490.2271-0.02190.50730.0183-0.23310.01560.0421-0.04080.04270.1780.05470.2695-5.6639-17.963451.0573
9912.5231-12.780616.602813.5361-19.11932.26790.14750.32510.0368-0.265-0.16550.01250.8167-0.0290.0180.1977-0.06090.01120.2669-0.01120.3176-16.973-4.309734.1288
1001.9170.4685-0.8811.83441.71434.45120.02090.3948-0.2172-0.0117-0.04450.45350.1656-0.06280.02360.139-0.0486-0.16780.3156-0.03410.5165-13.7197-14.151810.2436
1010.5780.3042-0.02262.8751-0.92251.1021-0.03-0.0836-0.0083-0.2403-0.00830.24120.0147-0.12670.03830.1063-0.0173-0.11670.04360.00650.15954.8065-20.72715.0899
1022.55031.78210.80713.43840.99462.52230.14590.0211-0.08680.0902-0.0470.29670.1094-0.1036-0.09890.11370.0107-0.03360.04450.04510.14912.8106-28.743424.9026
1039.33650.8411.51850.08530.13560.24960.0019-1.47840.0641-0.009-0.0510.0026-0.0245-0.24770.04910.45220.034-0.01750.87430.13770.7161.9251-20.180130.1452
1040.9905-0.26740.03581.44370.00952.07060.1211-0.008-0.0013-0.0345-0.04860.37520.0064-0.3238-0.07250.0726-0.0207-0.11920.07880.02490.3569-7.0045-11.696815.957
10510.93794.32360.98932.83950.77791.00720.31540.02670.23380.1214-0.10720.01810.19370.0924-0.20830.29920.03380.0050.08130.02750.147627.6455-10.4109-5.1581
1060.5586-0.3418-0.07961.9718-0.23941.2264-0.0662-0.0122-0.0868-0.23150.09330.0736-0.0137-0.0359-0.02710.1864-0.0131-0.05650.00530.00360.053721.382-19.7106-1.1697
1071.14380.9231-0.02955.4050.66920.66770.02450.11130.0366-0.4774-0.0550.0319-0.0342-0.110.03050.20410.0102-0.00830.12420.02150.071924.9395-7.5928-10.3159
10821.178414.7161-5.221610.7344-4.33472.2765-0.2260.40490.7162-0.0961-0.21350.01410.00850.63040.43950.8886-0.20140.17450.8775-0.0381.18728.5472-8.6347-17.5899
1091.86281.12343.59062.23283.036510.4946-0.01230.02570.1247-0.06840.0022-0.1468-0.2571-0.07730.01010.1553-0.03130.08090.10290.00040.230360.1403-7.49763.1727
1100.96960.21550.13711.0637-0.03761.23080.09730.0406-0.0919-0.43870.0277-0.2359-0.06070.0089-0.1250.23350.00720.09310.0467-0.05370.124352.6189-24.61595.3813
1110.60960.48690.5972.72630.0891.066-0.05130.196-0.0043-0.4690.1445-0.07220.13650.1408-0.09320.2996-0.02590.11280.1325-0.04180.161153.5709-8.6954-4.5986
1120.7771.3990.07386.97290.07980.8954-0.01450.2418-0.0539-0.30330.1154-0.5008-0.08590.1206-0.10090.14850.02220.110.179-0.05310.156966.8837-2.8673-4.2331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION11-8 - 13
2X-RAY DIFFRACTION2114 - 128
3X-RAY DIFFRACTION31129 - 165
4X-RAY DIFFRACTION41166 - 213
5X-RAY DIFFRACTION52-7 - 62
6X-RAY DIFFRACTION6263 - 148
7X-RAY DIFFRACTION72149 - 205
8X-RAY DIFFRACTION82206 - 225
9X-RAY DIFFRACTION9A11 - 130
10X-RAY DIFFRACTION10A131 - 182
11X-RAY DIFFRACTION11A183 - 223
12X-RAY DIFFRACTION12A224 - 252
13X-RAY DIFFRACTION13B2 - 47
14X-RAY DIFFRACTION14B48 - 63
15X-RAY DIFFRACTION15B64 - 179
16X-RAY DIFFRACTION16B180 - 249
17X-RAY DIFFRACTION17C2 - 48
18X-RAY DIFFRACTION18C49 - 64
19X-RAY DIFFRACTION19C65 - 175
20X-RAY DIFFRACTION20C176 - 245
21X-RAY DIFFRACTION21D3 - 48
22X-RAY DIFFRACTION22D49 - 65
23X-RAY DIFFRACTION23D66 - 210
24X-RAY DIFFRACTION24D211 - 243
25X-RAY DIFFRACTION25E9 - 30
26X-RAY DIFFRACTION26E31 - 83
27X-RAY DIFFRACTION27E84 - 140
28X-RAY DIFFRACTION28E141 - 250
29X-RAY DIFFRACTION29F3 - 81
30X-RAY DIFFRACTION30F82 - 126
31X-RAY DIFFRACTION31F127 - 172
32X-RAY DIFFRACTION32F173 - 234
33X-RAY DIFFRACTION33G4 - 162
34X-RAY DIFFRACTION34G163 - 175
35X-RAY DIFFRACTION35G176 - 207
36X-RAY DIFFRACTION36G208 - 247
37X-RAY DIFFRACTION37H1 - 17
38X-RAY DIFFRACTION38H18 - 84
39X-RAY DIFFRACTION39H85 - 147
40X-RAY DIFFRACTION40H148 - 196
41X-RAY DIFFRACTION41I1 - 45
42X-RAY DIFFRACTION42I46 - 75
43X-RAY DIFFRACTION43I76 - 198
44X-RAY DIFFRACTION44I199 - 221
45X-RAY DIFFRACTION45J-7 - 67
46X-RAY DIFFRACTION46J68 - 114
47X-RAY DIFFRACTION47J115 - 126
48X-RAY DIFFRACTION48J127 - 196
49X-RAY DIFFRACTION49K0 - 28
50X-RAY DIFFRACTION50K29 - 88
51X-RAY DIFFRACTION51K89 - 160
52X-RAY DIFFRACTION52K161 - 195
53X-RAY DIFFRACTION53L1 - 96
54X-RAY DIFFRACTION54L97 - 109
55X-RAY DIFFRACTION55L110 - 197
56X-RAY DIFFRACTION56L198 - 212
57X-RAY DIFFRACTION57M-8 - 17
58X-RAY DIFFRACTION58M18 - 126
59X-RAY DIFFRACTION59M127 - 164
60X-RAY DIFFRACTION60M165 - 213
61X-RAY DIFFRACTION61N-7 - 61
62X-RAY DIFFRACTION62N62 - 141
63X-RAY DIFFRACTION63N142 - 205
64X-RAY DIFFRACTION64N206 - 225
65X-RAY DIFFRACTION65O11 - 77
66X-RAY DIFFRACTION66O78 - 136
67X-RAY DIFFRACTION67O137 - 197
68X-RAY DIFFRACTION68O198 - 251
69X-RAY DIFFRACTION69P2 - 46
70X-RAY DIFFRACTION70P47 - 63
71X-RAY DIFFRACTION71P64 - 195
72X-RAY DIFFRACTION72P196 - 250
73X-RAY DIFFRACTION73Q2 - 44
74X-RAY DIFFRACTION74Q45 - 65
75X-RAY DIFFRACTION75Q66 - 177
76X-RAY DIFFRACTION76Q178 - 245
77X-RAY DIFFRACTION77R3 - 39
78X-RAY DIFFRACTION78R40 - 63
79X-RAY DIFFRACTION79R64 - 187
80X-RAY DIFFRACTION80R188 - 243
81X-RAY DIFFRACTION81S9 - 35
82X-RAY DIFFRACTION82S36 - 85
83X-RAY DIFFRACTION83S86 - 133
84X-RAY DIFFRACTION84S134 - 250
85X-RAY DIFFRACTION85T3 - 24
86X-RAY DIFFRACTION86T25 - 105
87X-RAY DIFFRACTION87T106 - 125
88X-RAY DIFFRACTION88T126 - 234
89X-RAY DIFFRACTION89U4 - 26
90X-RAY DIFFRACTION90U27 - 60
91X-RAY DIFFRACTION91U61 - 171
92X-RAY DIFFRACTION92U172 - 247
93X-RAY DIFFRACTION93V1 - 102
94X-RAY DIFFRACTION94V103 - 143
95X-RAY DIFFRACTION95V144 - 184
96X-RAY DIFFRACTION96V185 - 196
97X-RAY DIFFRACTION97W1 - 150
98X-RAY DIFFRACTION98W151 - 193
99X-RAY DIFFRACTION99W194 - 201
100X-RAY DIFFRACTION100W202 - 220
101X-RAY DIFFRACTION101X-7 - 67
102X-RAY DIFFRACTION102X68 - 114
103X-RAY DIFFRACTION103X115 - 126
104X-RAY DIFFRACTION104X127 - 196
105X-RAY DIFFRACTION105Y0 - 28
106X-RAY DIFFRACTION106Y29 - 159
107X-RAY DIFFRACTION107Y160 - 190
108X-RAY DIFFRACTION108Y191 - 195
109X-RAY DIFFRACTION109Z1 - 32
110X-RAY DIFFRACTION110Z33 - 96
111X-RAY DIFFRACTION111Z97 - 171
112X-RAY DIFFRACTION112Z172 - 212

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