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- PDB-6cty: Crystal structure of dihydroorotase pyrC from Yersinia pestis in ... -

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Basic information

Entry
Database: PDB / ID: 6cty
TitleCrystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution
ComponentsDihydroorotase
KeywordsHYDROLASE / Structural Genomics / dihydroorotase / zinc / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Dihydroorotase homodimeric type / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Amidohydrolase family / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Dihydroorotase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsLipowska, J. / Shabalin, I.G. / Winsor, J. / Woinska, M. / Cooper, D.R. / Kwon, K. / Shuvalova, L. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.
Authors: Lipowska, J. / Miks, C.D. / Kwon, K. / Shuvalova, L. / Zheng, H. / Lewinski, K. / Cooper, D.R. / Shabalin, I.G. / Minor, W.
History
DepositionMar 23, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionApr 4, 2018ID: 5V0G
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotase
B: Dihydroorotase
C: Dihydroorotase
D: Dihydroorotase
E: Dihydroorotase
F: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,88623
Polymers248,4316
Non-polymers1,45517
Water19,1681064
1
A: Dihydroorotase
E: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2067
Polymers82,8102
Non-polymers3965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-167 kcal/mol
Surface area25500 Å2
MethodPISA
2
B: Dihydroorotase
F: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3408
Polymers82,8102
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-171 kcal/mol
Surface area25100 Å2
MethodPISA
3
C: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3408
Polymers82,8102
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-170 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.838, 112.202, 208.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA5 - 34629 - 370
21PROPROVALVALBB5 - 34629 - 370
12GLNGLNVALVALAA4 - 34628 - 370
22GLNGLNVALVALCC4 - 34628 - 370
13PROPROVALVALAA5 - 34629 - 370
23PROPROVALVALDD5 - 34629 - 370
14PROPROARGARGAA5 - 34829 - 372
24PROPROARGARGEE5 - 34829 - 372
15PROPROLYSLYSAA5 - 34729 - 371
25PROPROLYSLYSFF5 - 34729 - 371
16PROPROVALVALBB5 - 34629 - 370
26PROPROVALVALCC5 - 34629 - 370
17PROPROLYSLYSBB5 - 34729 - 371
27PROPROLYSLYSDD5 - 34729 - 371
18PROPROLYSLYSBB5 - 34729 - 371
28PROPROLYSLYSEE5 - 34729 - 371
19PROPROVALVALBB5 - 34629 - 370
29PROPROVALVALFF5 - 34629 - 370
110PROPROVALVALCC5 - 34629 - 370
210PROPROVALVALDD5 - 34629 - 370
111PROPROVALVALCC5 - 34629 - 370
211PROPROVALVALEE5 - 34629 - 370
112PROPROVALVALCC5 - 34629 - 370
212PROPROVALVALFF5 - 34629 - 370
113PROPROLYSLYSDD5 - 34729 - 371
213PROPROLYSLYSEE5 - 34729 - 371
114PROPROVALVALDD5 - 34629 - 370
214PROPROVALVALFF5 - 34629 - 370
115PROPROARGARGEE5 - 34829 - 372
215PROPROARGARGFF5 - 34829 - 372

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Dihydroorotase / DHOase / Dihydroorotase pyrC


Mass: 41405.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: pyrC, YPO1587, y1746, YP_2265 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 "magic" / References: UniProt: Q8ZFU4, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1064 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL 10 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG 2 condition #67 (0.15 M DL-malic acid, pH 7.0, 20% w/v ...Details: 0.2 uL 10 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG 2 condition #67 (0.15 M DL-malic acid, pH 7.0, 20% w/v PEG3350), equilibrated against 1.3 M sodium chloride solution in 96-well 3-drop crystallization plate (Swissci)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923, 1.28241, 1.28908
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 12, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
21.282411
31.289081
ReflectionResolution: 2.4→50.01 Å / Num. obs: 81980 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Rsym value: 0.088 / Χ2: 0.864 / Net I/av σ(I): 16 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2.4-2.4460.6222.140790.7780.2650.680.6220.74294.1
2.44-2.495.90.60140900.7990.2580.6580.73994.9
2.49-2.535.60.49839800.8380.220.5480.75592.2
2.53-2.5960.46739920.8610.2010.5110.73993.1
2.59-2.646.40.40840900.8890.1690.4450.78194.3
2.64-2.76.40.3840530.930.1570.4131.01794.3
2.7-2.776.40.29240640.9380.1210.3180.78393.8
2.77-2.856.30.25640290.9470.1070.2790.79693.7
2.85-2.936.20.21740900.9570.0910.2370.81293.8
2.93-3.026.10.17840410.9670.0750.1940.82293.3
3.02-3.135.60.15139940.970.0670.1670.86491.8
3.13-3.266.40.12140450.9810.0510.1320.91993.2
3.26-3.416.40.09740840.9870.040.1060.93193.3
3.41-3.586.30.08940730.9860.0370.0971.12593.7
3.58-3.816.30.07240490.9910.0290.0781.07992.7
3.81-4.15.80.06240140.9920.0260.0681.08891.5
4.1-4.526.40.04841380.9950.0190.0520.95894
4.52-5.176.40.04641770.9950.0180.050.89194.6
5.17-6.515.90.04442730.9960.0180.0480.72695.1
6.51-505.90.03646250.9970.0150.0390.69498.6

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Processing

Software
NameVersionClassification
LAUEGENdata processing
SCALEPACKdata scaling
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EG6

2eg6


Resolution: 2.41→50.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.656 / SU ML: 0.174 / SU R Cruickshank DPI: 0.7587 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.759 / ESU R Free: 0.243 / SU Rfree Cruickshank DPI: 0.2443
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 3921 5 %RANDOM
Rwork0.1594 ---
obs0.1613 73934 88.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 226.09 Å2 / Biso mean: 44.305 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0 Å2
2---0.14 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.41→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16072 0 57 1064 17193
Biso mean--51.26 39.38 -
Num. residues----2069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916627
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215254
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.96522650
X-RAY DIFFRACTIONr_angle_other_deg0.859335285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43252072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11823.406737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.789152515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.44415113
X-RAY DIFFRACTIONr_chiral_restr0.0680.22576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023414
X-RAY DIFFRACTIONr_sphericity_bonded46.284512
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A112040.04
12B112040.04
21A112330.04
22C112330.04
31A112260.04
32D112260.04
41A109970.06
42E109970.06
51A112490.05
52F112490.05
61B111220.04
62C111220.04
71B111380.05
72D111380.05
81B110010.06
82E110010.06
91B111390.05
92F111390.05
101C111580.05
102D111580.05
111C109160.06
112E109160.06
121C111590.05
122F111590.05
131D110070.05
132E110070.05
141D112280.05
142F112280.05
151E110080.06
152F110080.06
LS refinement shellResolution: 2.408→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 201 -
Rwork0.217 4014 -
all-4215 -
obs--65.83 %
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)
13.1259-0.40830.15052.004-0.58011.75350.02270.1304-0.2176-0.2156-0.04380.13060.214-0.14490.0210.2029-0.0714-0.00860.0492-0.03530.0895.24552.096146.3
21.6791.11920.97853.92182.44952.71070.0517-0.3031-0.0070.3895-0.04950.44240.1676-0.3069-0.00230.2043-0.02160.07940.20310.06550.172810.56252.331163.966
31.2209-0.12410.27551.6066-0.22691.52330.01760.1144-0.1201-0.1644-0.0657-0.04040.20140.0950.04820.1584-0.02520.04750.0591-0.00530.042321.16158.494148.084
45.4484-3.2033-3.26756.76450.98176.00090.42570.35460.0722-0.5319-0.2820.2757-0.3796-0.1338-0.14360.2347-0.0756-0.080.16710.0320.10289.45564.275133.103
53.53210.1676-0.00192.18420.32682.5272-0.0177-0.24310.07680.26780.0363-0.1286-0.14220.2816-0.01870.21630.0222-0.03040.1730.03210.026551.12765.219143.278
627.0195-9.0317-0.32023.3206-1.10875.211-0.43960.00790.79310.22910.1361-0.2969-0.1298-0.35520.30350.4668-0.06220.12720.3933-0.00440.455258.46580.25134.682
71.3556-0.0050.15661.5364-0.38221.80020.1144-0.0805-0.00770.1782-0.1455-0.25730.06110.39090.03110.10710.0324-0.01650.13240.0310.048757.05867.216126.671
82.3283-0.1789-0.72141.65730.66291.57290.08410.101-0.41710.2292-0.20610.26090.4216-0.12820.12210.32940.0281-0.01960.15490.02990.203944.90753.282130.625
90.25140.53951.51471.1863.429610.28930.1672-0.0212-0.00910.2704-0.1316-0.00640.4725-0.7506-0.03570.53870.07310.08120.5727-0.03130.34485.41953.183116.997
101.3520.10670.17251.2683-0.47952.3982-0.0091-0.0508-0.1888-0.10460.02020.23760.339-0.6487-0.01120.1733-0.13410.01250.29160.00090.152212.43840.25779.828
112.2964-0.29880.09281.9824-0.53942.15520.0104-0.1498-0.00620.2417-0.1410.03710.1065-0.38650.13070.1365-0.08290.01270.15710.00320.042525.08744.9391.146
121.3098-0.0782-0.30472.6885-0.49142.6393-0.0136-0.2958-0.03440.58250.0470.2532-0.1437-0.5909-0.03330.2604-0.0680.14020.378-0.01190.204513.41145.632100.228
132.2449-1.9561-3.14695.87022.291110.33920.07620.3317-0.394-0.402-0.33-0.2540.6577-0.11780.25370.19060.0640.04350.18-0.00530.25465.09536.73676.944
141.3043-0.35360.355.11221.43313.3190.0819-0.1694-0.22440.1487-0.0029-0.13420.35060.1425-0.07890.1340.05920.00540.08780.08180.108163.79537.03896.011
152.4809-2.2026-0.62385.08880.54712.8727-0.0149-0.32220.0420.23130.0197-0.21240.10570.063-0.00470.2087-0.02560.01020.26680.04780.046361.76953.39999.828
161.8570.22780.04831.3642-0.19861.23780.01470.0253-0.1864-0.2016-0.0071-0.07130.2630.0615-0.00750.17010.03640.03010.03740.02810.048653.99644.58882.649
173.3990.0014-0.32552.2384-0.61383.6788-0.05970.22370.0399-0.0431-0.0479-0.11820.05430.1430.10750.1265-0.0183-0.05950.04110.0320.086623.344105.486144.378
188.49248.2493-3.64712.13232.426510.2811-1.08510.5521-0.4024-1.42540.8435-0.3122-0.18250.33440.24170.82970.2057-0.15511.017-0.2420.384536.48492.593133.385
191.0837-0.07830.16311.9545-0.19061.297-0.07030.02080.03070.0611-0.0358-0.2381-0.0870.17090.1060.1165-0.0388-0.05080.06670.01230.064829.64593.081153.639
204.17842.6130.7073.45842.40932.4456-0.1849-0.19230.3185-0.2644-0.30910.4638-0.4256-0.21860.4940.38380.0344-0.12150.12910.01030.26669.19498.672159.002
211.9583-1.0346-0.59131.75060.28892.16740.00590.15180.0341-0.097-0.07030.0891-0.0017-0.18950.06440.03320.0089-0.0140.07330.04460.063629.13583.15494.071
221.382-0.2907-0.10450.9870.41962.9955-0.01290.1470.163-0.1127-0.0349-0.1008-0.13830.26810.04770.0245-0.00090.01720.05490.04310.051547.37779.87499.934
232.0346-0.231-0.44621.9295-0.81272.750.01680.02320.49760.0418-0.1021-0.1598-0.52270.03860.08540.1143-0.0076-0.0290.03190.02930.171339.46493.87103.222
249.04145.0025-0.54248.063-2.06534.25510.0902-0.08510.21080.42360.02140.1216-0.4552-0.1974-0.11150.16060.0773-0.00590.1172-0.09090.114933.28494.61115.17
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 84
2X-RAY DIFFRACTION2A85 - 144
3X-RAY DIFFRACTION3A145 - 322
4X-RAY DIFFRACTION4A323 - 348
5X-RAY DIFFRACTION5B5 - 108
6X-RAY DIFFRACTION6B109 - 121
7X-RAY DIFFRACTION7B122 - 275
8X-RAY DIFFRACTION8B276 - 347
9X-RAY DIFFRACTION9C-5 - 12
10X-RAY DIFFRACTION10C13 - 203
11X-RAY DIFFRACTION11C204 - 275
12X-RAY DIFFRACTION12C276 - 347
13X-RAY DIFFRACTION13D5 - 18
14X-RAY DIFFRACTION14D19 - 84
15X-RAY DIFFRACTION15D85 - 128
16X-RAY DIFFRACTION16D129 - 347
17X-RAY DIFFRACTION17E5 - 112
18X-RAY DIFFRACTION18E113 - 121
19X-RAY DIFFRACTION19E122 - 309
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