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- PDB-2wpd: The Mg.ADP inhibited state of the yeast F1c10 ATP synthase -

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Basic information

Entry
Database: PDB / ID: 2wpd
TitleThe Mg.ADP inhibited state of the yeast F1c10 ATP synthase
Components(ATP SYNTHASE SUBUNIT ...) x 6
KeywordsHYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP-BINDING / CENTRAL STALK / ATP SYNTHESIS / PHOSPHOPROTEIN / MEMBRANE PROTEIN / LIPID-BINDING / ION TRANSPORT / NUCLEOTIDE-BINDING / HYDROGEN ION TRANSPORT
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) ...mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / 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 / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin / Thrombin, subunit H - #170 ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / 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, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / 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 / Helix Hairpins / 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 / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.432 Å
AuthorsDautant, A. / Velours, J. / Giraud, M.-F.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of the Mg.Adp-Inhibited State of the Yeast F1C10-ATP Synthase.
Authors: Dautant, A. / Velours, J. / Giraud, M.
#1: Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase.
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#2: Journal: Embo J. / Year: 2006
Title: Novel Features of the Rotary Catalytic Mechanism Revealed in the Structure of Yeast F1 ATPase.
Authors: Kabaleeswaran, V. / Puri, N. / Walker, J.E. / Leslie, A.G.W. / Mueller, D.M.
#3: Journal: J.Biol.Chem. / Year: 2009
Title: Asymmetric Structure of the Yeast F1 ATPase in the Absence of Bound Nucleotides.
Authors: Kabaleeswaran, V. / Shen, H. / Symersky, J. / Walker, J.E. / Leslie, A.G.W. / Mueller, D.M.
#4: Journal: Science / Year: 2005
Title: Structure of the Rotor Ring of F-Type Na+-ATPase from Ilyobacter Tartaricus.
Authors: Meier, T. / Polzer, P. / Diederichs, K. / Welte, W. / Dimroth, P.
#5: Journal: J.Bioenerg.Biomembr. / Year: 2009
Title: Hydrogenated and Fluorinated Surfactants Derived from Tris(Hydroxymethyl)-Acrylamidomethane Allow the Purification of a Highly Active Yeast F1-F0 ATP-Synthase with an Enhanced Stability.
Authors: Talbot, J.-C. / Dautant, A. / Polidori, A. / Pucci, B. / Cohen-Bouhacina, T. / Maali, A. / Salin, B. / Brethes, D. / Velours, J. / Giraud, M.-F.
History
DepositionAug 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,52829
Polymers448,03019
Non-polymers2,49710
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32020 Å2
ΔGint-390 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.990, 173.944, 137.016
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN J AND (RESID 1:34 OR RESID 44:76)
211CHAIN K AND (RESID 1:34 OR RESID 44:76)
311CHAIN L AND (RESID 1:34 OR RESID 44:76)
411CHAIN M AND (RESID 1:34 OR RESID 44:76)
511CHAIN N AND (RESID 1:34 OR RESID 44:76)
611CHAIN O AND (RESID 1:34 OR RESID 44:76)
711CHAIN P AND (RESID 1:34 OR RESID 44:76)
811CHAIN Q AND (RESID 1:34 OR RESID 44:76)
911CHAIN R AND (RESID 1:34 OR RESID 44:76)
1011CHAIN S AND (RESID 1:34 OR RESID 44:76)

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Components

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ATP SYNTHASE SUBUNIT ... , 6 types, 19 molecules ABCDEFGHIJKLMNOPQRS

#1: Protein ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL / / ATP SYNTHASE ALPHA CHAIN\ / MITOCHONDRIAL


Mass: 55007.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: P07251
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL / / ATP SYNTHASE BETA CHAIN\ / MITOCHONDRIAL


Mass: 51181.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A
References: UniProt: P00830, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / / ATP SYNTHASE GAMMA CHAIN\ / MITOCHONDRIAL / F-ATPASE GAMMA SUBUNIT


Mass: 30657.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: P38077
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / / ATP SYNTHASE DELTA CHAIN\ / MITOCHONDRIAL / F-ATPASE DELTA SUBUNIT


Mass: 14565.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: Q12165
#5: Protein ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / / ATP SYNTHASE EPSILON CHAIN\ / MITOCHONDRIAL


Mass: 6618.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-62 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: P21306
#6: Protein
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL / / ATP SYNTHASE 9 CHAIN\ / MITOCHONDRIAL / LIPID-BINDING PROTEIN / OLIGOMYCIN RESISTANCE PROTEIN 1


Mass: 7762.375 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A
References: UniProt: P61829, H+-transporting two-sector ATPase

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Non-polymers , 3 types, 10 molecules

#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.67 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES/HCL PH 7.5, 12% PEG MME 5000, 100 MM SODIUM CHLORIDE MIXED 1:1 WITH PROTEIN SOLUTION CONTAINING 0.64 MM DDM, 25 MM TRIS/HCL PH 8.0, 100 MM SODIUM CHLORIDE, 25 MM TREHALOSE, 0.5 ...Details: 0.1 M HEPES/HCL PH 7.5, 12% PEG MME 5000, 100 MM SODIUM CHLORIDE MIXED 1:1 WITH PROTEIN SOLUTION CONTAINING 0.64 MM DDM, 25 MM TRIS/HCL PH 8.0, 100 MM SODIUM CHLORIDE, 25 MM TREHALOSE, 0.5 MM EDTA, 0.02% SODIUM AZIDE, 2 MM MAGNESIUM CHLORIDE, 0.66 MM ADP, 0.1 MM DCCD, 2.5 MM DTT, 0.5 MM PMSF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.43→39.8 Å / Num. obs: 84424 / % possible obs: 88.1 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.3
Reflection shellResolution: 3.43→3.62 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.3 / % possible all: 64.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HLD, 1YCE

2hld

1yce


Resolution: 3.432→39.775 Å / SU ML: 0.67 / σ(F): 1.34 / Phase error: 32.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 3767 5.1 %
Rwork0.2863 --
obs0.2868 74395 88.13 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.559 Å2 / ksol: 0.281 e/Å3
Displacement parametersBiso mean: 108 Å2
Baniso -1Baniso -2Baniso -3
1-7.3833 Å20 Å228.4471 Å2
2---13.2772 Å20 Å2
3---5.8939 Å2
Refinement stepCycle: LAST / Resolution: 3.432→39.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30674 0 152 0 30826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431294
X-RAY DIFFRACTIONf_angle_d0.62942421
X-RAY DIFFRACTIONf_dihedral_angle_d16.7111370
X-RAY DIFFRACTIONf_chiral_restr0.0325046
X-RAY DIFFRACTIONf_plane_restr0.0035446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11J480X-RAY DIFFRACTIONPOSITIONAL
12K480X-RAY DIFFRACTIONPOSITIONAL0
13L480X-RAY DIFFRACTIONPOSITIONAL0
14M480X-RAY DIFFRACTIONPOSITIONAL0
15N480X-RAY DIFFRACTIONPOSITIONAL0
16O480X-RAY DIFFRACTIONPOSITIONAL0
17P480X-RAY DIFFRACTIONPOSITIONAL0
18Q480X-RAY DIFFRACTIONPOSITIONAL0
19R480X-RAY DIFFRACTIONPOSITIONAL0
110S480X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4323-3.47570.4065900.39681770X-RAY DIFFRACTION60
3.4757-3.52140.37311040.39962004X-RAY DIFFRACTION68
3.5214-3.56960.39731130.39532063X-RAY DIFFRACTION69
3.5696-3.62060.361180.37292044X-RAY DIFFRACTION70
3.6206-3.67460.34891070.36042100X-RAY DIFFRACTION71
3.6746-3.7320.38561240.3752622X-RAY DIFFRACTION88
3.732-3.79310.37131230.37572688X-RAY DIFFRACTION90
3.7931-3.85840.34221520.35442708X-RAY DIFFRACTION91
3.8584-3.92850.35341410.34822690X-RAY DIFFRACTION92
3.9285-4.0040.37941550.34332739X-RAY DIFFRACTION93
4.004-4.08570.31741330.33492772X-RAY DIFFRACTION93
4.0857-4.17440.3541460.32082771X-RAY DIFFRACTION93
4.1744-4.27140.31371420.31652782X-RAY DIFFRACTION94
4.2714-4.37810.34771490.30172765X-RAY DIFFRACTION94
4.3781-4.49630.30851470.2952797X-RAY DIFFRACTION94
4.4963-4.62850.31591370.26982786X-RAY DIFFRACTION94
4.6285-4.77760.28651470.26632811X-RAY DIFFRACTION94
4.7776-4.94810.27811610.26272792X-RAY DIFFRACTION94
4.9481-5.14580.24341520.25952804X-RAY DIFFRACTION95
5.1458-5.37940.28311630.26162782X-RAY DIFFRACTION94
5.3794-5.66230.2671470.2642810X-RAY DIFFRACTION94
5.6623-6.01590.29271580.26112763X-RAY DIFFRACTION94
6.0159-6.47860.30341570.25962797X-RAY DIFFRACTION93
6.4786-7.12720.25331590.24022747X-RAY DIFFRACTION93
7.1272-8.15080.24531530.20572762X-RAY DIFFRACTION93
8.1508-10.24010.17511500.1722759X-RAY DIFFRACTION92
10.2401-39.77730.23971390.25472700X-RAY DIFFRACTION88

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