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- PDB-7mvs: DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A re... -

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Basic information

Entry
Database: PDB / ID: 7mvs
TitleDNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA gyrase subunit B,DNA gyrase subunit A
KeywordsISOMERASE/DNA/ANTIBIOTIC / Inhibitor / Complex / DNA / Gyrase / ANTIBIOTIC / ISOMERASE-DNA-ANTIBIOTIC complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #40 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...Gyrase A; domain 2 - #40 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Gyrase A; domain 2 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-Y1W / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.60137142659 Å
AuthorsRatigan, S.C. / McElroy, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA.
Authors: Lu, Y. / Vibhute, S. / Li, L. / Okumu, A. / Ratigan, S.C. / Nolan, S. / Papa, J.L. / Mann, C.A. / English, A. / Chen, A. / Seffernick, J.T. / Koci, B. / Duncan, L.R. / Roth, B. / Cummings, J. ...Authors: Lu, Y. / Vibhute, S. / Li, L. / Okumu, A. / Ratigan, S.C. / Nolan, S. / Papa, J.L. / Mann, C.A. / English, A. / Chen, A. / Seffernick, J.T. / Koci, B. / Duncan, L.R. / Roth, B. / Cummings, J.E. / Slayden, R.A. / Lindert, S. / McElroy, C.A. / Wozniak, D.J. / Yalowich, J. / Mitton-Fry, M.J.
History
DepositionMay 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: DNA gyrase subunit B,DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit A
C: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
D: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,38711
Polymers168,6044
Non-polymers7837
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration provides evidence that Chain A is dimerized with Chain B., There's density in the crystal structure revealing that dsDNA is bound to gyrase dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-118 kcal/mol
Surface area57100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.017, 93.017, 406.663
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DADADCDC(chain 'C' and ((resid 1 and (name C5' or name...CC1 - 191 - 19
211DADADCDCchain 'D'DD1 - 191 - 19
112LYSLYSTHRTHR(chain 'A' and (resid 10 through 19 or (resid 20...AA10 - 3610 - 36
122SERSERSERSER(chain 'A' and (resid 10 through 19 or (resid 20...AA38 - 4238 - 42
132THRTHRASNASN(chain 'A' and (resid 10 through 19 or (resid 20...AA44 - 6844 - 68
142GLUGLUTYRTYR(chain 'A' and (resid 10 through 19 or (resid 20...AA70 - 11870 - 118
152PHEPHEMETMET(chain 'A' and (resid 10 through 19 or (resid 20...AA120 - 121120 - 121
162PROPROILEILE(chain 'A' and (resid 10 through 19 or (resid 20...AA123 - 125123 - 125
172ALAALAALAALA(chain 'A' and (resid 10 through 19 or (resid 20...AA127 - 173127 - 173
182GLNGLNTYRTYR(chain 'A' and (resid 10 through 19 or (resid 20...AA175 - 198175 - 198
192ARGARGMETMET(chain 'A' and (resid 10 through 19 or (resid 20...AA209 - 219210 - 220
1102GLUGLULEULEU(chain 'A' and (resid 10 through 19 or (resid 20...AA221 - 224222 - 225
1112TYRTYRLYSLYS(chain 'A' and (resid 10 through 19 or (resid 20...AA226 - 263227 - 264
1122TYRTYRVALVAL(chain 'A' and (resid 10 through 19 or (resid 20...AA265 - 272266 - 273
1132VALVALASPASP(chain 'A' and (resid 10 through 19 or (resid 20...AA275 - 284276 - 285
1142SERSERTYRTYR(chain 'A' and (resid 10 through 19 or (resid 20...AA286 - 288287 - 289
1152ALAALAVALVAL(chain 'A' and (resid 10 through 19 or (resid 20...AA290 - 292291 - 293
1162METMETALAALA(chain 'A' and (resid 10 through 19 or (resid 20...AA294 - 321295 - 322
1172ARGARGLEULEU(chain 'A' and (resid 10 through 19 or (resid 20...AA323 - 337324 - 338
1182ASPASPILEILE(chain 'A' and (resid 10 through 19 or (resid 20...AA339 - 340340 - 341
1192LYSLYSALAALA(chain 'A' and (resid 10 through 19 or (resid 20...AA342 - 373343 - 374
1202GLYGLYGLYGLY(chain 'A' and (resid 10 through 19 or (resid 20...AA375 - 427376 - 428
1212GLYGLYILEILE(chain 'A' and (resid 10 through 19 or (resid 20...AA430 - 431431 - 432
1222ALAALATYRTYR(chain 'A' and (resid 10 through 19 or (resid 20...AA434 - 435435 - 436
1232THRTHRTHRTHR(chain 'A' and (resid 10 through 19 or (resid 20...AA437438
1242GLYGLYASPASP(chain 'A' and (resid 10 through 19 or (resid 20...AA440 - 492441 - 493
1252ARGARGLEULEU(chain 'A' and (resid 10 through 19 or (resid 20...AA494 - 499495 - 500
1262THRTHRVALVAL(chain 'A' and (resid 10 through 19 or (resid 20...AA501 - 509502 - 510
1272LYSLYSLEULEU(chain 'A' and (resid 10 through 19 or (resid 20...AA511 - 557512 - 558
1282HISHISALAALA(chain 'A' and (resid 10 through 19 or (resid 20...AA559 - 579560 - 580
1292ILEILEASPASP(chain 'A' and (resid 10 through 19 or (resid 20...AA581 - 593582 - 594
1302ILEILESERSER(chain 'A' and (resid 10 through 19 or (resid 20...AA595 - 619596 - 620
1312LYSLYSLEULEU(chain 'A' and (resid 10 through 19 or (resid 20...AA621 - 650622 - 651
1322TYRTYRGLUGLU(chain 'A' and (resid 10 through 19 or (resid 20...AA652 - 664653 - 665
1332LEULEULEULEU(chain 'A' and (resid 10 through 19 or (resid 20...AA666 - 691667 - 692
212LYSLYSTHRTHR(chain 'B' and (resid 10 through 36 or resid 38...BB10 - 3610 - 36
222SERSERSERSER(chain 'B' and (resid 10 through 36 or resid 38...BB38 - 4238 - 42
232THRTHRASNASN(chain 'B' and (resid 10 through 36 or resid 38...BB44 - 6844 - 68
242GLUGLUTYRTYR(chain 'B' and (resid 10 through 36 or resid 38...BB70 - 11870 - 118
252PHEPHEMETMET(chain 'B' and (resid 10 through 36 or resid 38...BB120 - 121120 - 121
262PROPROILEILE(chain 'B' and (resid 10 through 36 or resid 38...BB123 - 125123 - 125
272ALAALAALAALA(chain 'B' and (resid 10 through 36 or resid 38...BB127 - 173127 - 173
282GLNGLNTYRTYR(chain 'B' and (resid 10 through 36 or resid 38...BB175 - 198175 - 198
292ARGARGMETMET(chain 'B' and (resid 10 through 36 or resid 38...BB209 - 219210 - 220
2102GLUGLULEULEU(chain 'B' and (resid 10 through 36 or resid 38...BB221 - 224222 - 225
2112TYRTYRLYSLYS(chain 'B' and (resid 10 through 36 or resid 38...BB226 - 263227 - 264
2122TYRTYRVALVAL(chain 'B' and (resid 10 through 36 or resid 38...BB265 - 272266 - 273
2132VALVALASPASP(chain 'B' and (resid 10 through 36 or resid 38...BB275 - 284276 - 285
2142SERSERTYRTYR(chain 'B' and (resid 10 through 36 or resid 38...BB286 - 288287 - 289
2152ALAALAVALVAL(chain 'B' and (resid 10 through 36 or resid 38...BB290 - 292291 - 293
2162METMETALAALA(chain 'B' and (resid 10 through 36 or resid 38...BB294 - 321295 - 322
2172ARGARGLEULEU(chain 'B' and (resid 10 through 36 or resid 38...BB323 - 337324 - 338
2182ASPASPILEILE(chain 'B' and (resid 10 through 36 or resid 38...BB339 - 340340 - 341
2192LYSLYSALAALA(chain 'B' and (resid 10 through 36 or resid 38...BB342 - 373343 - 374
2202GLYGLYGLYGLY(chain 'B' and (resid 10 through 36 or resid 38...BB375 - 427376 - 428
2212GLYGLYILEILE(chain 'B' and (resid 10 through 36 or resid 38...BB430 - 431431 - 432
2222ALAALATYRTYR(chain 'B' and (resid 10 through 36 or resid 38...BB434 - 435435 - 436
2232THRTHRTHRTHR(chain 'B' and (resid 10 through 36 or resid 38...BB437438
2242GLYGLYASPASP(chain 'B' and (resid 10 through 36 or resid 38...BB440 - 492441 - 493
2252ARGARGLEULEU(chain 'B' and (resid 10 through 36 or resid 38...BB494 - 499495 - 500
2262THRTHRVALVAL(chain 'B' and (resid 10 through 36 or resid 38...BB501 - 509502 - 510
2272LYSLYSLEULEU(chain 'B' and (resid 10 through 36 or resid 38...BB511 - 557512 - 558
2282HISHISALAALA(chain 'B' and (resid 10 through 36 or resid 38...BB559 - 579560 - 580
2292ILEILEASPASP(chain 'B' and (resid 10 through 36 or resid 38...BB581 - 593582 - 594
2302ILEILESERSER(chain 'B' and (resid 10 through 36 or resid 38...BB595 - 619596 - 620
2312LYSLYSLEULEU(chain 'B' and (resid 10 through 36 or resid 38...BB621 - 650622 - 651
2322TYRTYRGLUGLU(chain 'B' and (resid 10 through 36 or resid 38...BB652 - 664653 - 665
2332LEULEULEULEU(chain 'B' and (resid 10 through 36 or resid 38...BB666 - 691667 - 692

NCS ensembles :
ID
1
2

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein DNA gyrase subunit B,DNA gyrase subunit A


Mass: 78166.055 Da / Num. of mol.: 2 / Mutation: Y324F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, gyrA, SA0006 / Plasmid: pDB.His.MBP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A0K8, UniProt: Q99XG5, DNA topoisomerase (ATP-hydrolysing)
#2: DNA chain DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 6135.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 152 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-Y1W / (1S)-2-[(2r,5S)-5-{[(2,3-dihydro-1,4-benzodioxin-6-yl)methyl]amino}-1,3-dioxan-2-yl]-1-(3-fluoro-6-methoxyquinolin-4-yl)ethan-1-ol


Mass: 470.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27FN2O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.16 % / Description: 40umx150um hexagonal rods, clear
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: motherliquor: 80mM Bis-Tris, pH=6.2, 15.33% PEG 5000MME protein: 50mM HEPES, pH=7.5 1.2uL motherliquor : 0.8uL protein streaked with existing seed stock
Temp details: +/- 4K

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.601→23.7427486328 Å / Num. obs: 60022 / % possible obs: 98.87 % / Redundancy: 6.1 % / Biso Wilson estimate: 61.3801855894 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.093 / Rrim(I) all: 0.239 / Net I/σ(I): 9.2
Reflection shellResolution: 2.601→2.694 Å / Num. unique obs: 5472 / CC1/2: 0.389 / Rpim(I) all: 0.66 / % possible all: 90.81

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS

2xcs


Resolution: 2.60137142659→23.7427486328 Å / SU ML: 0.459867161797 / Cross valid method: NONE / σ(F): 1.33788961277 / Phase error: 29.4972337594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251722343658 3878 3.30506668939 %
Rwork0.195513593603 113457 -
obs0.19732038353 60022 97.216123286 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.4825563237 Å2
Refinement stepCycle: LAST / Resolution: 2.60137142659→23.7427486328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10627 800 44 145 11616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032970553182112147
X-RAY DIFFRACTIONf_angle_d0.50740740559816605
X-RAY DIFFRACTIONf_chiral_restr0.04010037139261849
X-RAY DIFFRACTIONf_plane_restr0.003005588907092069
X-RAY DIFFRACTIONf_dihedral_angle_d17.13741821967354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6014-2.63310.413692904439990.3408981582092668X-RAY DIFFRACTION64.5891690009
2.6331-2.66630.3285688998421230.3488150189823645X-RAY DIFFRACTION85.9881332725
2.6663-2.70140.3976294485941290.3566511895243706X-RAY DIFFRACTION90.1716435457
2.7014-2.73830.4185377903381320.3408945935214002X-RAY DIFFRACTION94.4482522276
2.7383-2.77740.3800307969021320.330739388043932X-RAY DIFFRACTION96.1665877899
2.7774-2.81880.3836278561221390.3068963495454172X-RAY DIFFRACTION96.7242539825
2.8188-2.86280.3407783618171380.2990332337694041X-RAY DIFFRACTION99.3108365019
2.8628-2.90960.3641622963281380.2882653296794128X-RAY DIFFRACTION99.8128217127
2.9096-2.95970.3532973147971400.2696587252694160X-RAY DIFFRACTION99.6292863763
2.9597-3.01340.3323797930361500.2532938790794156X-RAY DIFFRACTION99.8376999768
3.0134-3.07130.3001460915351520.2423493001484141X-RAY DIFFRACTION99.8372093023
3.0713-3.13380.3173548467581500.2361694472184176X-RAY DIFFRACTION99.8614958449
3.1338-3.20180.2670409649441460.219332522154204X-RAY DIFFRACTION99.7706422018
3.2018-3.27610.2892847222511440.2147177542424088X-RAY DIFFRACTION99.7877858996
3.2761-3.35780.3048877430511340.2086153860714217X-RAY DIFFRACTION99.8393758605
3.3578-3.44830.2401469396361430.1992458984754164X-RAY DIFFRACTION99.4688221709
3.4483-3.54950.2307060918071360.1865420599314110X-RAY DIFFRACTION99.8823806163
3.5495-3.66360.267053911211420.1745296007174156X-RAY DIFFRACTION99.9534883721
3.6636-3.79410.2231246176761460.1694216809474155X-RAY DIFFRACTION99.883882954
3.7941-3.94530.2385026985921490.1649024225474171X-RAY DIFFRACTION99.907493062
3.9453-4.1240.2226448570651500.1595759368094134X-RAY DIFFRACTION99.7903563941
4.124-4.34020.2092273940531360.1562616540664171X-RAY DIFFRACTION99.7452524317
4.3402-4.61030.2021171587431400.1495926195614192X-RAY DIFFRACTION99.5633187773
4.6103-4.96320.1956535439651420.1458476958114132X-RAY DIFFRACTION99.9532273152
4.9632-5.45720.2118010204681330.1630490576744199X-RAY DIFFRACTION99.8386725052
5.4572-6.23430.2173743176711380.1798435983514167X-RAY DIFFRACTION99.7220291869
6.2343-7.8080.2211023029081360.1915019631734136X-RAY DIFFRACTION99.5340167754
7.808-23.74274863280.2404376318611410.1874013597594134X-RAY DIFFRACTION99.1649269311

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