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- PDB-2gl8: Human Retinoic acid receptor RXR-gamma ligand-binding domain -

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Basic information

Entry
Database: PDB / ID: 2gl8
TitleHuman Retinoic acid receptor RXR-gamma ligand-binding domain
ComponentsRetinoic acid receptor RXR-gamma
KeywordsHormone/Growth factor receptor / nuclear receptor / Structural Genomics / Structural Genomics Consortium / SGC / Hormone-Growth factor receptor COMPLEX
Function / homology
Function and homology information


retinoic acid-responsive element binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / response to retinoic acid / molecular condensate scaffold activity / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding ...retinoic acid-responsive element binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / response to retinoic acid / molecular condensate scaffold activity / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / cytoplasm
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Ligand-binding domain of nuclear hormone receptor / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoic acid receptor RXR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMin, J.R. / Schuetz, A. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Retinoic acid receptor RXR-gamma ligand-binding domain.
Authors: Schuetz, A. / Min, J.R. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-gamma
B: Retinoic acid receptor RXR-gamma
C: Retinoic acid receptor RXR-gamma
D: Retinoic acid receptor RXR-gamma


Theoretical massNumber of molelcules
Total (without water)107,9844
Polymers107,9844
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.070, 161.316, 68.682
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Retinoic acid receptor RXR-gamma / Retinoid X receptor gamma


Mass: 26995.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRG, NR2B3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus RIL / References: UniProt: P48443
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: peg, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→80.58 Å / Num. all: 37858 / Num. obs: 37858 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RDT
Resolution: 2.4→80.58 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 20.822 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29574 1936 5.1 %RANDOM
Rwork0.24266 ---
all0.24528 36107 --
obs0.24528 36107 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.588 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-1.11 Å2
2---1.27 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 0 105 5916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225912
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9837991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28423.289225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.054151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.871541
X-RAY DIFFRACTIONr_chiral_restr0.1070.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024340
X-RAY DIFFRACTIONr_nbd_refined0.2090.22690
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.24
X-RAY DIFFRACTIONr_mcbond_it0.5771.53919
X-RAY DIFFRACTIONr_mcangle_it1.01626050
X-RAY DIFFRACTIONr_scbond_it1.38432228
X-RAY DIFFRACTIONr_scangle_it2.2184.51941
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 150 -
Rwork0.26 2470 -
obs--92.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
111.8556-11.4799-8.360311.62176.554210.59250.19130.0355-0.34670.7833-0.0696-0.2162-0.03440.1342-0.12170.0934-0.0818-0.20080.11770.06430.151414.20411.98829.1767
27.9841-0.9898-5.05855.1577.294212.03442.01720.4038-1.0178-1.6919-1.91251.0096-1.5793-1.4091-0.10470.55310.2154-0.26930.41670.00880.00025.217818.793511.8109
36.5856-2.1714-2.093.1851-3.46177.641-0.22690.04650.15360.7333-0.0546-0.4147-0.32170.28040.28150.0806-0.0911-0.14730.11070.0330.150118.979911.65216.5955
417.96176.53361.0434.5146-0.79223.0149-0.24970.27680.64680.0850.0066-0.052-0.4487-0.08260.24320.126-0.0376-0.1440.0470.06570.160812.747218.0381-0.0322
511.44093.0562-3.90269.5323-3.44671.9944-0.33890.0863-0.24980.72140.8236-0.6365-0.3329-0.5109-0.48460.08340.0081-0.0560.14770.08040.0531-1.61178.78555.1916
624.8449-16.26178.310612.6096-5.890314.285-0.389-0.57250.53620.91950.88070.31590.24-0.5236-0.49170.00140.00360.08410.2210.1223-0.0194-10.349713.2447.7494
75.367-3.95330.65215.5789-2.00882.27240.0919-0.0382-0.1613-0.13420.3830.10710.2628-0.557-0.47490.0096-0.0836-0.03680.1870.13120.1218-6.96547.8998-0.9649
80.4923-0.31921.54642.7641-1.28584.8891-0.12730.0029-0.185-0.08260.1025-0.3530.15590.02230.02480.041-0.0284-0.0790.11940.06920.165511.27256.9782-1.3034
95.9927-5.9965-2.178228.8184-6.45936.0971-0.15020.34470.4865-0.3409-0.2802-1.46110.03720.64540.4304-0.0221-0.1025-0.1270.13890.09390.228521.95512.4939-7.3163
100.8977-0.42291.09832.6474-1.64241.91270.0764-0.0264-0.14620.0090.10720.00560.2313-0.0758-0.18360.1357-0.0285-0.08660.07330.06920.16547.3083-2.0041-4.0018
1125.3842-6.5281-0.72931.5946-6.2261.39590.40160.69420.4629-0.70760.9260.04410.0628-1.3976-1.32750.0679-0.0758-0.04080.29320.08160.0848-0.610918.527-7.4139
120.25740.62240.18071.50490.4370.12690.39220.7914-1.17351.67420.1170.5254-0.64631.0144-0.50920.55220.29440.17630.4986-0.01310.1722-7.063127.89023.985
133.2043-3.4593.34197.9536-5.52818.46760.22210.2631-0.2257-0.7565-0.145-0.25740.87920.4991-0.07710.3133-0.0102-0.07990.0559-0.1139-0.04152.2677-2.2275-31.2173
142.37090.67760.43523.0616-1.07464.88830.43280.1589-0.5142-0.6143-0.160.08330.4879-0.327-0.27280.2574-0.0817-0.21370.0592-0.05060.0726-7.1355-0.4601-28.8217
1516.67216.2848-3.91722.6593-0.95851.84550.05040.15360.2269-0.52090.05720.3286-0.0811-0.0573-0.10760.1577-0.0326-0.10730.09330.04050.0495-3.52618.9307-24.1915
168.45645.6202-6.407922.7798-14.216510.06220.13340.6709-0.2844-0.6985-0.46860.74250.99260.81380.33530.1590.06630.0250.2242-0.0497-0.038411.21759.3254-28.9973
1710.7917-5.0777-2.956118.74122.73179.57030.05880.65770.1148-1.0937-0.0417-0.5237-0.31670.8477-0.01710.0221-0.09230.10080.19990.1813-0.092214.530818.267-31.5368
1814.989-8.83034.439118.6899-10.006212.6659-0.2077-0.42420.5970.08380.1603-0.8955-0.67060.41220.04730.0906-0.19120.01590.09080.06080.105111.88521.1121-21.9789
190.16031.2077-0.297410.54770.86737.2321-0.12220.43320.1401-0.2925-0.2558-0.31370.12281.08070.3780.00220.02810.06730.25280.11620.145416.36666.0027-22.2156
205.3723-2.8267-1.53742.5550.18182.80650.0633-0.013-0.1508-0.2070.2640.20250.5071-0.2473-0.32730.1665-0.1032-0.12830.07120.04820.1076-2.7682-1.2082-17.4933
2131.74493.5237-1.75794.4508-2.53211.44260.9294-0.0053-1.1702-0.4604-0.2762-0.57691.4430.6228-0.65320.380.2588-0.11830.0629-0.07950.282414.6206-9.407-18.6534
222.3982-3.01180.94423.8306-1.53632.91740.14090.27910.1217-0.2696-0.1772-0.0020.14780.27490.03630.0723-0.0554-0.0510.1290.04190.121610.69053.6307-14.6141
2310.0271-2.8293-9.32098.0702-14.133647.30910.2439-0.053-0.2414-0.6304-0.0320.48260.0093-0.0143-0.21190.1942-0.09240.1029-0.00530.00410.0872.496118.5816-17.751
241.5793-5.0988.494216.4563-27.419245.68540.4229-0.01940.44841.50021.15151.3218-1.5912-1.7952-1.57440.89060.21430.41910.1850.3716-0.1962.12228.4733-31.7363
2510.9861-3.16347.19817.994-3.28424.9234-0.0927-0.3990.40411.2365-0.1270.2521-0.0004-0.48580.21970.23070.0651-0.04620.1062-0.18980.0616-9.393958.93052.8176
261.8197-7.0284.515128.6285-15.058815.0147-1.5909-1.05781.57711.9750.4033-3.90810.17350.5991.18750.43870.1338-0.29210.1372-0.16130.4396-0.425245.17918.6501
274.46963.22960.15272.8034-1.04325.5849-0.26-0.39390.05420.98920.34140.19750.1856-0.5809-0.08140.1572-0.02060.13040.1046-0.03190.0209-15.072846.23684.3371
2819.576211.9841-1.96558.33020.40292.79340.2275-0.37440.0831.0355-0.1093-0.54510.51080.1362-0.11820.1397-0.0004-0.09120.0452-0.03470.13810.606445.5849-2.8704
295.0623-1.64670.456712.17983.09157.73380.2034-0.35980.50630.66840.3385-1.66610.54490.943-0.5419-0.09150.0297-0.26580.1082-0.06730.518213.382343.7278-3.5251
302.6705-1.40691.20947.43931.91763.27590.06740.23490.374-0.33070.0247-1.0131-0.12140.2152-0.092-0.0337-0.03910.00810.0424-0.01350.29956.044448.8443-11.2905
313.2148-1.69081.07073.12452.42214.3437-0.1202-0.1779-0.01730.2839-0.0684-0.07560.001-0.3160.18860.0476-0.0298-0.00510.1173-0.05380.0781-9.385951.0607-4.9
3212.6064-18.8581-1.23242.8024-3.06278.7768-0.4603-0.5738-0.99220.10430.88873.36050.8436-1.1248-0.4284-0.1425-0.26150.09330.2909-0.10310.3026-21.954143.1249-5.1424
335.13266.9991-2.570211.8377-0.45245.3493-0.10890.16670.1734-0.18860.0369-0.0411-0.386-0.71520.0720.0370.1094-0.03090.1035-0.08740.1584-14.055358.1277-7.9176
345.3532.35910.616412.44424.52671.6586-0.2670.17850.2967-0.63710.2028-0.0837-0.3695-0.04780.06430.20640.0061-0.0378-0.00170.01330.1762-4.772463.241-14.0148
351.5953-0.14582.073210.5728-0.38852.69780.16310.2227-0.040.0478-0.2389-0.3840.2344-0.02360.07580.072-0.03470.00780.1231-0.03940.1122-3.073142.8024-12.7966
360.8269-2.23492.10226.0408-5.68215.34470.0948-1.04160.03940.51650.0854-0.1107-0.2058-0.7226-0.18020.6295-0.0766-0.52720.01370.13460.297810.256529.47411.3889
371.60733.7705-1.35830.56291.99945.39750.16670.1345-0.0617-1.0371-0.85450.4279-0.3613-0.38570.68780.3030.2029-0.13310.18430.0206-0.1627-13.779447.8818-37.2702
388.9013-6.2425-4.906828.0903-4.06795.08280.54140.28510.0277-2.0695-0.35150.39180.7379-0.5491-0.18990.42730.0424-0.08320.06470.0139-0.2035-8.415541.1679-38.3906
3914.8144-6.06372.854211.9154-1.28211.98410.10870.86170.7284-0.7492-0.4595-0.6751-0.76960.30250.35080.36140.00290.150.08480.158-0.10110.081148.692-37.3322
4011.811.5905-3.76260.8259-1.05493.47670.29310.1034-0.2265-0.5972-0.38180.03150.468-0.21750.08870.164-0.0345-0.02750.1219-0.06630.0327-9.620639.1271-28.9575
4114.9292-12.0832.014728.7379-2.117223.19920.19660.3617-0.1601-0.20340.19230.18210.6416-1.5442-0.3889-0.0576-0.562-0.23260.2432-0.07130.0306-24.678930.1561-26.3935
427.0943-8.50651.656543.541-4.75842.94230.381-0.74-0.5748-0.0221-0.13021.10060.8939-1.1075-0.25080.0694-0.34990.02060.2565-0.08710.0983-19.646932.5567-17.967
432.0915-2.70691.57617.1254-0.96511.5066-0.0161-0.3273-0.1096-0.564-0.23180.6951-0.4806-0.84250.24790.01890.0348-0.18220.4362-0.18880.1408-23.343647.9959-23.9189
4413.5209-2.53542.05993.70162.00332.08380.176-0.32590.0109-1.0422-0.0389-0.2982-0.0912-0.0859-0.13710.1514-0.02250.11370.07590.03350.0479-4.288947.0996-26.9059
4515.8365-4.02190.9055.08041.77393.2194-0.05370.17610.8882-0.5412-0.0922-0.6725-0.7221-0.09950.14590.24520.00340.0841-0.0310.08050.0456-4.22355.9583-26.8297
461.19241.97066.255913.64288.864833.02930.1924-0.11770.8721-1.6304-1.25431.5418-0.6246-0.61981.06190.20850.3802-0.19160.2046-0.09850.1734-22.154360.6229-22.5531
470.7848-0.3791.01297.37323.12573.1246-0.02520.0361-0.10120.0644-0.00040.3120.2289-0.52670.02570.0467-0.0586-0.02850.1702-0.01440.1155-12.106444.0451-18.3638
481.2418-3.0596-0.117187.637835.350815.3590.54980.41770.565-2.6906-0.7388-1.5118-0.8931-0.01650.18890.6555-0.1516-0.0969-0.0625-0.2560.008-12.321714.5029-29.9647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 2411 - 24
2X-RAY DIFFRACTION2AA25 - 5825 - 58
3X-RAY DIFFRACTION3AA59 - 7359 - 73
4X-RAY DIFFRACTION4AA74 - 8874 - 88
5X-RAY DIFFRACTION5AA89 - 9789 - 97
6X-RAY DIFFRACTION6AA98 - 11698 - 116
7X-RAY DIFFRACTION7AA117 - 143117 - 143
8X-RAY DIFFRACTION8AA144 - 158144 - 158
9X-RAY DIFFRACTION9AA159 - 171159 - 171
10X-RAY DIFFRACTION10AA172 - 207172 - 207
11X-RAY DIFFRACTION11AA208 - 211208 - 211
12X-RAY DIFFRACTION12AA212 - 224212 - 224
13X-RAY DIFFRACTION13BB11 - 5511 - 55
14X-RAY DIFFRACTION14BB56 - 7556 - 75
15X-RAY DIFFRACTION15BB76 - 9176 - 91
16X-RAY DIFFRACTION16BB92 - 9692 - 96
17X-RAY DIFFRACTION17BB97 - 11897 - 118
18X-RAY DIFFRACTION18BB119 - 129119 - 129
19X-RAY DIFFRACTION19BB130 - 143130 - 143
20X-RAY DIFFRACTION20BB144 - 178144 - 178
21X-RAY DIFFRACTION21BB179 - 189179 - 189
22X-RAY DIFFRACTION22BB190 - 207190 - 207
23X-RAY DIFFRACTION23BB208 - 211208 - 211
24X-RAY DIFFRACTION24BB212 - 226212 - 226
25X-RAY DIFFRACTION25CC11 - 2311 - 23
26X-RAY DIFFRACTION26CC24 - 5924 - 59
27X-RAY DIFFRACTION27CC60 - 8360 - 83
28X-RAY DIFFRACTION28CC84 - 9684 - 96
29X-RAY DIFFRACTION29CC97 - 12097 - 120
30X-RAY DIFFRACTION30CC121 - 143121 - 143
31X-RAY DIFFRACTION31CC144 - 157144 - 157
32X-RAY DIFFRACTION32CC158 - 169158 - 169
33X-RAY DIFFRACTION33CC170 - 183170 - 183
34X-RAY DIFFRACTION34CC184 - 198184 - 198
35X-RAY DIFFRACTION35CC199 - 211199 - 211
36X-RAY DIFFRACTION36CC212 - 227212 - 227
37X-RAY DIFFRACTION37DD11 - 5311 - 53
38X-RAY DIFFRACTION38DD54 - 6354 - 63
39X-RAY DIFFRACTION39DD64 - 7564 - 75
40X-RAY DIFFRACTION40DD76 - 9776 - 97
41X-RAY DIFFRACTION41DD98 - 11798 - 117
42X-RAY DIFFRACTION42DD118 - 134118 - 134
43X-RAY DIFFRACTION43DD135 - 144135 - 144
44X-RAY DIFFRACTION44DD145 - 163145 - 163
45X-RAY DIFFRACTION45DD164 - 182164 - 182
46X-RAY DIFFRACTION46DD183 - 192183 - 192
47X-RAY DIFFRACTION47DD193 - 212193 - 212
48X-RAY DIFFRACTION48DD213 - 228213 - 228

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