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- PDB-5hkk: Caldalaklibacillus thermarum F1-ATPase (wild type) -

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Basic information

Entry
Database: PDB / ID: 5hkk
TitleCaldalaklibacillus thermarum F1-ATPase (wild type)
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / F1-ATPase / Complex
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha
Similarity search - Component
Biological speciesCaldalkalibacillus thermarum TA2.A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsFerguson, S.A. / Cook, G.M. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Funding support United Kingdom, New Zealand, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U1065663150 United Kingdom
Medical Research Council (United Kingdom)U105184325 United Kingdom
Medical Research Council (United Kingdom)MR/M009858/1 United Kingdom
James Cook Fellowship New Zealand
Health Research Council New Zealand
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum.
Authors: Ferguson, S.A. / Cook, G.M. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Oct 12, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
I: ATP synthase subunit alpha
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit beta
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase gamma chain
P: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,24245
Polymers725,52816
Non-polymers6,71429
Water5,152286
1
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,16723
Polymers362,7648
Non-polymers3,40315
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41910 Å2
ΔGint-260 kcal/mol
Surface area108600 Å2
MethodPISA
2
I: ATP synthase subunit alpha
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit beta
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase gamma chain
P: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,07522
Polymers362,7648
Non-polymers3,31114
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41870 Å2
ΔGint-261 kcal/mol
Surface area108410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.820, 130.790, 210.390
Angle α, β, γ (deg.)90.000, 107.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23I
14A
24J
15A
25K
16B
26C
17B
27I
18B
28J
19B
29K
110C
210I
111C
211J
112C
212K
113D
213E
114D
214F
115D
215L
116D
216M
117D
217N
118E
218F
119E
219L
120E
220M
121E
221N
122F
222L
123F
223M
124F
224N
125G
225O
126H
226P
127I
227J
128I
228K
129J
229K
130L
230M
131L
231N
132M
232N

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
11GLUGLUTHRTHRAA27 - 49927 - 499
21GLUGLUTHRTHRBB27 - 49927 - 499
12GLUGLUTHRTHRAA27 - 49927 - 499
22GLUGLUTHRTHRCC27 - 49927 - 499
13GLUGLUTHRTHRAA27 - 49927 - 499
23GLUGLUTHRTHRII27 - 49927 - 499
14GLUGLUTHRTHRAA27 - 49927 - 499
24GLUGLUTHRTHRJJ27 - 49927 - 499
15VALVALTHRTHRAA26 - 49926 - 499
25VALVALTHRTHRKK26 - 49926 - 499
16GLUGLUPROPROBB27 - 50027 - 500
26GLUGLUPROPROCC27 - 50027 - 500
17GLUGLUTHRTHRBB27 - 49927 - 499
27GLUGLUTHRTHRII27 - 49927 - 499
18GLUGLUSERSERBB27 - 50127 - 501
28GLUGLUSERSERJJ27 - 50127 - 501
19GLUGLUPROPROBB27 - 50027 - 500
29GLUGLUPROPROKK27 - 50027 - 500
110GLUGLUTHRTHRCC27 - 49927 - 499
210GLUGLUTHRTHRII27 - 49927 - 499
111GLUGLUPROPROCC27 - 50027 - 500
211GLUGLUPROPROJJ27 - 50027 - 500
112GLUGLUSERSERCC27 - 50127 - 501
212GLUGLUSERSERKK27 - 50127 - 501
113ASNASNLEULEUDD2 - 4622 - 462
213ASNASNLEULEUEE2 - 4622 - 462
114ASNASNLEULEUDD2 - 4622 - 462
214ASNASNLEULEUFF2 - 4622 - 462
115ASNASNLEULEUDD2 - 4622 - 462
215ASNASNLEULEULL2 - 4622 - 462
116ASNASNLEULEUDD2 - 4622 - 462
216ASNASNLEULEUMM2 - 4622 - 462
117ASNASNLEULEUDD2 - 4622 - 462
217ASNASNLEULEUNN2 - 4622 - 462
118ASNASNLEULEUEE2 - 4622 - 462
218ASNASNLEULEUFF2 - 4622 - 462
119ASNASNLEULEUEE2 - 4622 - 462
219ASNASNLEULEULL2 - 4622 - 462
120ASNASNLEULEUEE2 - 4622 - 462
220ASNASNLEULEUMM2 - 4622 - 462
121ASNASNLEULEUEE2 - 4622 - 462
221ASNASNLEULEUNN2 - 4622 - 462
122ASNASNLEULEUFF2 - 4622 - 462
222ASNASNLEULEULL2 - 4622 - 462
123ASNASNLEULEUFF2 - 4622 - 462
223ASNASNLEULEUMM2 - 4622 - 462
124ASNASNLEULEUFF2 - 4622 - 462
224ASNASNLEULEUNN2 - 4622 - 462
125GLYGLYARGARGGG3 - 2863 - 286
225GLYGLYARGARGOO3 - 2863 - 286
126THRTHRLYSLYSHH3 - 1343 - 134
226THRTHRLYSLYSPP3 - 1343 - 134
127GLUGLUTHRTHRII27 - 49927 - 499
227GLUGLUTHRTHRJJ27 - 49927 - 499
128GLUGLUTHRTHRII27 - 49927 - 499
228GLUGLUTHRTHRKK27 - 49927 - 499
129GLUGLUPROPROJJ27 - 50027 - 500
229GLUGLUPROPROKK27 - 50027 - 500
130ASNASNLEULEULL2 - 4622 - 462
230ASNASNLEULEUMM2 - 4622 - 462
131ASNASNLEULEULL2 - 4622 - 462
231ASNASNLEULEUNN2 - 4622 - 462
132ASNASNLEULEUMM2 - 4622 - 462
232ASNASNLEULEUNN2 - 4622 - 462

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32

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Components

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ATP synthase ... , 4 types, 16 molecules ABCIJKDEFLMNGOHP

#1: Protein
ATP synthase subunit alpha / / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55016.609 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpA, CathTA2_2809 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: F5LA74, H+-transporting two-sector ATPase
#2: Protein
ATP synthase subunit beta / / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50266.012 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpD, CathTA2_2807 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: F5LA72, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31932.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpG, CathTA2_2808 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: F5LA73
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14983.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpC, CathTA2_2806 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: F5LA71

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Non-polymers , 6 types, 315 molecules

#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 295 K / Method: microbatch / Details: PEG 4600, PEG 1500, ADP, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→64.3 Å / Num. obs: 145626 / % possible obs: 95.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3 / Num. unique all: 19744 / % possible all: 88.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0144refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ck3

2ck3


Resolution: 3→62.16 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2138 / WRfactor Rwork: 0.1726 / FOM work R set: 0.822 / SU B: 21.61 / SU ML: 0.366 / SU Rfree: 0.4606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 7274 5 %RANDOM
Rwork0.2029 ---
obs0.2051 138025 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.96 Å2 / Biso mean: 50.934 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å2-0 Å20.9 Å2
2---2.28 Å2-0 Å2
3---3.95 Å2
Refinement stepCycle: final / Resolution: 3→62.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49525 0 414 286 50225
Biso mean--44.62 31.22 -
Num. residues----6451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01950767
X-RAY DIFFRACTIONr_bond_other_d0.0020.0249434
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.99268898
X-RAY DIFFRACTIONr_angle_other_deg0.9873113828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12956435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79524.3872234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.077158855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.49915380
X-RAY DIFFRACTIONr_chiral_restr0.090.27862
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02157273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210793
X-RAY DIFFRACTIONr_mcbond_it2.714.97525788
X-RAY DIFFRACTIONr_mcbond_other2.714.97525787
X-RAY DIFFRACTIONr_mcangle_it4.4157.45932257
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A278660.1
12B278660.1
21A279940.11
22C279940.11
31A299100.02
32I299100.02
41A279000.1
42J279000.1
51A280240.11
52K280240.11
61B284140.1
62C284140.1
71B278980.1
72I278980.1
81B299560.01
82J299560.01
91B284320.1
92K284320.1
101C280080.11
102I280080.11
111C284120.1
112J284120.1
121C301560.02
122K301560.02
131D263280.11
132E263280.11
141D274480.09
142F274480.09
151D287300.02
152L287300.02
161D263540.12
162M263540.12
171D274600.09
172N274600.09
181E264320.11
182F264320.11
191E263240.11
192L263240.11
201E288860.01
202M288860.01
211E264380.11
212N264380.11
221F274700.09
222L274700.09
231F264300.11
232M264300.11
241F287660.01
242N287660.01
251G180600.02
252O180600.02
261H76780.04
262P76780.04
271I279280.1
272J279280.1
281I279960.11
282K279960.11
291J284180.1
292K284180.1
301L263480.12
302M263480.12
311L274840.09
312N274840.09
321M264420.11
322N264420.11
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 505 -
Rwork0.342 9324 -
all-9829 -
obs--87.19 %

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