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- PDB-2qw4: Human NR4A1 ligand-binding domain -

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Basic information

Entry
Database: PDB / ID: 2qw4
TitleHuman NR4A1 ligand-binding domain
ComponentsOrphan nuclear receptor NR4A1
KeywordsHORMONE RECEPTOR / NUCLEAR RECEPTOR / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / DNA-binding / Metal-binding / Nucleus / Phosphorylation / Transcription / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear receptor / 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / 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 / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Crystal Structure of Human Nr4A1 Ligand-Binding Domain
Authors: Min, J.R. / Schuetz, A. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionAug 9, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionAug 21, 2007ID: 2GBD
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 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: Orphan nuclear receptor NR4A1
B: Orphan nuclear receptor NR4A1
C: Orphan nuclear receptor NR4A1
D: Orphan nuclear receptor NR4A1


Theoretical massNumber of molelcules
Total (without water)121,0804
Polymers121,0804
Non-polymers00
Water18010
1
A: Orphan nuclear receptor NR4A1


Theoretical massNumber of molelcules
Total (without water)30,2701
Polymers30,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Orphan nuclear receptor NR4A1


Theoretical massNumber of molelcules
Total (without water)30,2701
Polymers30,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Orphan nuclear receptor NR4A1


Theoretical massNumber of molelcules
Total (without water)30,2701
Polymers30,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Orphan nuclear receptor NR4A1


Theoretical massNumber of molelcules
Total (without water)30,2701
Polymers30,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.530, 96.364, 144.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Orphan nuclear receptor NR4A1 / Orphan nuclear receptor HMR / Early response protein NAK1 / TR3 orphan receptor / ST-59


Mass: 30270.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22736
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 15 % PEG 6000, 0.1 M BISTRIS PH 6.4, 0.4 M SODIUM THIOCYANATE, AND 5 % ETHYLENGLYCOL, pH 6.80, 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 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2006
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 31070 / % possible obs: 98.9 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yje
Resolution: 2.8→48.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 36.243 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.971 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1566 5.1 %RANDOM
Rwork0.23 ---
obs0.233 29394 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7137 0 0 10 7147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9979856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5823.257304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.785151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1711555
X-RAY DIFFRACTIONr_chiral_restr0.1040.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.23540
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25036
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.631.54647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14827294
X-RAY DIFFRACTIONr_scbond_it1.69532891
X-RAY DIFFRACTIONr_scangle_it2.7954.52562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 114 -
Rwork0.285 2083 -
obs-2083 97.08 %
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)
13.4074-2.6311-3.03142.03172.34082.697-0.39140.07710.85110.0072-0.4091-0.9227-1.16080.63070.80040.1348-0.0984-0.07320.12620.09240.27426.640829.7298-9.3384
24.6334-0.54570.12821.86961.01280.58880.1117-0.3422-0.16790.1224-0.0627-0.03790.0234-0.0273-0.0490.1787-0.1019-0.13120.12990.13890.177830.886816.347414.0357
35.2103-1.71590.71561.6581-1.29384.0522-0.0042-0.36070.10470.25670.1088-0.0867-0.48770.1463-0.10460.1377-0.02510.01190.07490.00480.113718.514925.8915-0.1329
41.46-0.68032.29611.44110.48666.49120.0831-0.1289-0.3162-0.00560.1243-0.38180.28880.0942-0.20740.09540.0186-0.07110.0650.08090.201829.511411.25376.0573
59.1685-3.2066-2.93831.20961.44934.24420.3971-0.1127-0.2188-0.4267-0.18930.1731-0.009-0.2077-0.20770.1094-0.0067-0.02320.11530.07940.165615.649121.7011-7.676
69.60441.1821-6.38161.22571.41098.70590.25240.5348-0.0514-0.3474-0.18240.3225-0.07480.0769-0.070.0990.06590.00550.11210.06030.14877.757628.7916-12.684
71.83290.9237-1.2210.85231.25959.8990.05480.77410.1656-0.43060.096-0.2587-0.82180.4074-0.15070.11440.01840.01830.2371-0.01720.098921.544321.2104-20.767
82.2354-2.07183.92671.9766-3.67116.91550.39080.1385-0.3212-0.1819-0.3012-0.1670.42510.1251-0.08960.2134-0.0354-0.09420.1209-0.02390.227517.266811.3519-9.3993
94.64111.8829-1.7764.5274-1.02775.3033-0.1858-0.0961-0.50290.47060.1394-0.04840.5271-0.31660.04650.1757-0.0931-0.07010.11120.15710.144514.685110.796714.6491
1014.36241.00636.54955.90010.46244.93790.8171-0.7247-0.1827-0.1693-0.18050.7019-0.601-0.63-0.63660.2856-0.04560.09480.0175-0.0870.075612.940220.443716.2699
114.07031.3998-3.56894.3025-3.34635.4818-0.4295-0.2838-0.4033-0.0839-0.1914-0.87810.43310.47640.62090.04770.0048-0.00750.12160.03220.154536.9562-20.3383-10.1967
1216.62118.698316.283323.677916.175417.6904-1.3268-0.46750.05750.6951.14520.37651.42552.19670.18160.19930.05440.16410.62420.2620.199533.2358-2.566-31.5437
131.23471.6022-4.97276.1712-9.776222.72630.44440.1796-0.2219-0.2525-0.63120.0240.49410.23860.18680.150.01320.01560.11770.01130.11928.5452-16.9981-26.5835
143.62981.4532-1.81353.2259-0.29930.9749-0.19540.0509-0.29640.0270.00030.03020.2317-0.03010.1950.17420.01180.00840.06930.00610.154720.9703-28.4707-12.0543
155.01181.5163-2.31721.350.09281.77850.5335-0.24420.14960.0782-0.337-0.0406-0.06630.1997-0.19650.1252-0.0261-0.02630.10030.03810.202129.8162-13.5996-11.1461
161.09070.1584-0.36852.7392-1.30782.53770.1116-0.12460.18560.044-0.1254-0.0626-0.24720.17050.01380.1075-0.01230.00810.05590.02470.148529.1423-11.1568-12.1783
178.8564.30332.58046.41072.10653.9050.2978-1.19880.30220.7037-0.7287-0.03150.7802-0.86730.43080.041-0.01820.14780.12530.02150.235516.0736-24.86881.9092
1817.71915.82388.737528.9582-28.59540.92130.4947-1.3599-0.09530.6921-1.2554-0.8398-2.6853-1.7330.76060.0310.10240.04870.1836-0.09090.300319.3939-10.35752.4576
191.26491.54632.41634.19450.11038.1254-0.0960.04170.1038-0.13250.24250.1296-0.2025-0.0163-0.14650.13460.0724-0.02040.11640.00620.170317.8-9.9533-22.6795
207.30856.00821.41411.2025-4.17074.8147-0.0956-0.4468-0.1521-1.00380.48990.67580.79630.2326-0.39430.2066-0.0033-0.02530.0321-0.02990.167117.7259-20.0523-28.2355
212.06952.60694.667210.6693.993711.0069-0.12730.02240.1386-0.2234-0.36250.6683-0.2119-0.97650.48970.14410.1611-0.08980.0325-0.08950.2247-9.63867.7875-51.3301
224.8229-3.3532.76413.1978-3.85565.8995-0.0922-0.07040.70720.035-0.11690.241-0.2616-0.80260.20910.19920.0336-0.07610.1637-0.1310.0938-2.853317.0824-26.7201
232.97075.0705-4.83939.0527-8.36327.9101-0.2953-0.244-1.06621.1731-0.3387-0.9602-1.27470.0470.63410.31290.0252-0.13510.19410.05090.1635.20384.6111-16.4407
245.2713-0.18094.69531.28311.28619.59690.0444-0.3462-0.203-0.00740.01090.24150.0454-0.7138-0.05530.13560.046-0.0330.0297-0.06470.1973-6.627-0.2122-34.3112
251.54821.28550.9544.47441.03841.5825-0.03840.1151-0.17740.16790.0798-0.2259-0.151-0.1051-0.04140.1297-0.0052-0.08520.0979-0.06280.1429-2.77240.5421-41.0828
268.547-2.19284.19133.3153-0.72654.28990.047-0.338-0.43070.1145-0.38130.1743-0.1022-0.30940.33430.20520.0127-0.07340.1557-0.08580.06612.371510.4938-26.6109
271.0340.47870.190.7153-0.47022.0129-0.10010.1009-0.0457-0.1840.0333-0.0789-0.20520.0540.06680.14970.0569-0.0810.0622-0.01840.13712.3120.8771-47.2982
287.8918-2.3107-1.73636.16840.83780.4018-0.18881.09850.34840.5647-0.5661-0.0902-0.62150.54790.75490.2246-0.0991-0.06170.10710.04740.14095.91097.988-55.6342
292.52621.42541.00694.2037-1.70256.0379-0.02-0.12120.0529-0.21040.07540.08670.45160.9329-0.05540.11080.0335-0.04490.03640.00120.15969.7746-3.6407-31.3051
301.9061-0.8310.21741.2306-1.7083.0217-0.1288-0.1621-0.14170.00570.26810.66330.2564-0.0629-0.13940.1861-0.0501-0.09750.05350.07120.31580.7908-9.3987-26.2318
312.57020.44012.76090.2417-0.36637.1992-0.1048-0.0170.28930.1513-0.2728-0.2373-0.3290.29550.37770.1276-0.1225-0.07920.15880.00920.140248.992916.2856-49.3267
3219.8894-18.03776.478517.4743-2.133614.6575-0.9761.04872.47610.489-0.1856-0.3274-1.40091.02381.16160.5206-0.2499-0.19730.03870.00690.353237.62195.5458-70.3904
331.88260.8126-1.52770.6443-0.63791.24130.01030.1388-0.6674-0.25060.058-0.68770.03960.7664-0.06830.1225-0.10220.00930.13390.03310.259651.64593.8146-52.2531
341.1662-2.5179-1.96495.67173.49625.6741-0.9422-0.0319-0.44410.44770.3790.51970.57231.22110.56320.10030.0070.10460.20440.20550.262653.3364-3.8079-40.7192
351.7453-2.23560.32253.4762-0.52644.76780.04480.0204-0.14980.07070.0189-0.1969-0.29130.0032-0.06370.0483-0.099-0.00630.1085-0.00020.194542.193313.1286-53.0675
362.90450.00620.71391.0584-0.04554.08490.0267-0.089-0.08280.0282-0.1034-0.0072-0.275-0.02950.07670.1021-0.1231-0.03710.08070.01990.13239.38049.3831-44.6125
374.4875-3.743-3.10368.49042.34394.607-0.2893-0.6392-0.34860.80060.10690.24690.01940.72170.18240.0739-0.1346-0.02580.24010.25490.085946.29391.3718-29.1966
3817.934-14.8673-4.290812.32513.55711.02661.27290.5142-0.6014-1.544-2.21360.7784-0.30520.26840.94070.3968-0.09240.11460.06390.03310.041635.48675.6407-36.5333
390.08090.77341.14447.572410.926416.1878-0.05830.1565-0.21010.4050.15480.0220.8216-0.4155-0.09650.1159-0.18590.06670.1881-0.06430.206536.8247-2.8775-54.0699
404.54970.95260.36419.0354-1.91161.9388-0.02750.0815-0.3581-0.3842-0.1096-0.96751.38460.96340.13710.01210.01290.0260.0147-0.0950.280746.4449-7.7555-57.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 4638 - 52
2X-RAY DIFFRACTION2AA47 - 8353 - 89
3X-RAY DIFFRACTION3AA84 - 12690 - 132
4X-RAY DIFFRACTION4AA127 - 163133 - 169
5X-RAY DIFFRACTION5AA164 - 190170 - 196
6X-RAY DIFFRACTION6AA191 - 199197 - 205
7X-RAY DIFFRACTION7AA200 - 213206 - 219
8X-RAY DIFFRACTION8AA217 - 235223 - 241
9X-RAY DIFFRACTION9AA236 - 247242 - 253
10X-RAY DIFFRACTION10AA248 - 264254 - 270
11X-RAY DIFFRACTION11BB32 - 5938 - 65
12X-RAY DIFFRACTION12BB60 - 6966 - 75
13X-RAY DIFFRACTION13BB70 - 8276 - 88
14X-RAY DIFFRACTION14BB83 - 11489 - 120
15X-RAY DIFFRACTION15BB115 - 126121 - 132
16X-RAY DIFFRACTION16BB127 - 183133 - 189
17X-RAY DIFFRACTION17BB184 - 213190 - 219
18X-RAY DIFFRACTION18BB217 - 229223 - 235
19X-RAY DIFFRACTION19BB230 - 248236 - 254
20X-RAY DIFFRACTION20BB249 - 264255 - 270
21X-RAY DIFFRACTION21CC30 - 4436 - 50
22X-RAY DIFFRACTION22CC45 - 6151 - 67
23X-RAY DIFFRACTION23CC62 - 7468 - 80
24X-RAY DIFFRACTION24CC75 - 9181 - 97
25X-RAY DIFFRACTION25CC92 - 13098 - 136
26X-RAY DIFFRACTION26CC131 - 149137 - 155
27X-RAY DIFFRACTION27CC150 - 203156 - 209
28X-RAY DIFFRACTION28CC204 - 228210 - 234
29X-RAY DIFFRACTION29CC229 - 247235 - 253
30X-RAY DIFFRACTION30CC248 - 264254 - 270
31X-RAY DIFFRACTION31DD32 - 6238 - 68
32X-RAY DIFFRACTION32DD63 - 7069 - 76
33X-RAY DIFFRACTION33DD71 - 9377 - 99
34X-RAY DIFFRACTION34DD94 - 114100 - 120
35X-RAY DIFFRACTION35DD115 - 145121 - 151
36X-RAY DIFFRACTION36DD146 - 182152 - 188
37X-RAY DIFFRACTION37DD183 - 223189 - 229
38X-RAY DIFFRACTION38DD224 - 229230 - 235
39X-RAY DIFFRACTION39DD230 - 247236 - 253
40X-RAY DIFFRACTION40DD248 - 265254 - 271

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