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- PDB-3mdt: Voriconazole complex of Cytochrome P450 46A1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3mdt
TitleVoriconazole complex of Cytochrome P450 46A1
ComponentsCholesterol 24-hydroxylase
KeywordsOXIDOREDUCTASE / CYP46A1 / P450 46A1 / P450 / VORICONAZOLE / MONOOXYGENASE / METABOLIC ENZYME / HEME / Cholesterol metabolism / Endoplasmic reticulum / Iron / Lipid metabolism / Membrane / Metal-binding / Microsome / NADP / Steroid metabolism / Transmembrane
Function / homology
Function and homology information


cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity ...cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity / Endogenous sterols / cholesterol catabolic process / xenobiotic metabolic process / presynapse / nervous system development / postsynapse / iron ion binding / dendrite / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Cholesterol 24-hydroxylase / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Voriconazole / Cholesterol 24-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMast, N. / Charvet, C. / Pikuleva, I. / Stout, C.D.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain.
Authors: Mast, N. / Charvet, C. / Pikuleva, I.A. / Stout, C.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principal cholesterol hydroxylase in the brain.
Authors: Mast, N. / White, M.A. / Bjorkhem, I. / Johnson, E.F. / Stout, C.D. / Pikuleva, I.A.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 10, 2014Group: Non-polymer description
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholesterol 24-hydroxylase
B: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1826
Polymers104,2502
Non-polymers1,9324
Water6,810378
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A: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0913
Polymers52,1251
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0913
Polymers52,1251
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.600, 121.600, 143.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cholesterol 24-hydroxylase / CH24H / Cytochrome P450 46A1


Mass: 52125.086 Da / Num. of mol.: 2 / Fragment: UNP residues 51-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46A1, CYP46 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9Y6A2, EC: 1.14.13.98
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-VOR / Voriconazole / (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol


Mass: 349.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14F3N5O / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 8% PEG 8000, 20% glycerol, 50 mM KPi, 0.03% undecylmaltoside, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2009 / Details: Rh coated flat mirror
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11-H, K, -L20.5
ReflectionResolution: 2.3→92.86 Å / Num. all: 45803 / Num. obs: 45803 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6719 / Rsym value: 0.392 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q9F
Resolution: 2.3→92.86 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.84 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.563 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY TWO TWIN DOMAINS: H,K,L TWIN FRACTION 0.500 -H,K,-L TWIN FRACTION 0.500 20 TLS GROUPS REFINED PER CHAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2325 5.1 %RANDOM
Rwork0.229 ---
all0.232 45787 --
obs0.232 43462 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 50.84 Å2 / Biso mean: 35.1 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2---1.05 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→92.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6836 0 136 378 7350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0217966
X-RAY DIFFRACTIONr_angle_refined_deg0.8541.96112204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3067.51688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03223.193332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.494151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4881568
X-RAY DIFFRACTIONr_chiral_restr0.0680.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218836
X-RAY DIFFRACTIONr_mcbond_it0.2071.54226
X-RAY DIFFRACTIONr_mcangle_it0.3826830
X-RAY DIFFRACTIONr_scbond_it0.41832896
X-RAY DIFFRACTIONr_scangle_it0.7164.52802
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 150 -
Rwork0.228 3251 -
all-3401 -
obs-3251 99.88 %
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)
10.97720.291600.3763-0.49980.8636-0.0062-0.04320.01470.04620.00470.0071-0.008-0.00030.00160.1615-0.0008-0.0010.1621-0.00080.160514.2047-39.4256-25.9672
20.0475-0.0302-0.05160.02610.01760.0895-0.005-0.06640.04520.0730.00330.0842-0.0458-0.07730.00160.2024-0.0004-0.00030.201700.20259.7138-45.5715-26.2428
30.4019-0.03460.25860.2484-0.06380.17340.00120.0374-0.009-0.0103-0.00120.0912-0.0015-0.10860.00010.1919-0.00080.00010.1867-0.00070.19153.2369-45.6458-39.2289
40.5552-0.4044-0.19430.29450.14150.0680.0023-0.0220.02320.0349-0.01250.067-0.0298-0.06750.01030.2364-0.00170.00010.23470.00130.2352-9.7989-34.0485-25.4377
50.31490.14980.04760.9259-0.21550.2636-0.0080.03930.0333-0.05930.01480.0021-0.01540.0025-0.00690.19480.00360.00050.2034-0.00390.2004-9.7652-30.8804-44.4868
60.50850.0155-0.12140.6779-0.17860.5417-0.02670.03730.0767-0.01520.0116-0.0141-0.08270.06010.01520.17150.00630.00690.1698-0.00070.17354.3294-7.9059-35.0538
70.3630.2753-0.15630.28040.05960.50990.0126-0.0713-0.07910.0447-0.01-0.01160.08250.017-0.00250.21040.00120.00090.2157-0.00460.2156-5.4977-15.5029-27.6747
80.3595-0.35340.16080.3473-0.1580.0719-0.0284-0.1502-0.00450.15850.0251-0.09030.03030.05830.00340.2741-0.00420.00120.27460.00030.2767-8.9056-25.2837-17.4568
90.40640.02450.02290.01720.10330.6644-0.00420.0654-0.0047-0.06770.00810.06150.0101-0.0716-0.0040.25720.00060.00040.2579-0.00030.2616-20.626-19.1225-39.9573
100.0958-0.31750.00051.0514-0.00051.22160.00140.0038-0.0536-0.0026-0.00190.15670.0894-0.16190.00050.15890.00840.00040.12510.00010.1259-2.3689-22.4587-34.3394
110.55150.1864-0.32710.5187-0.06280.41660.0070.10110.0661-0.1034-0.02090.0027-0.02270.03730.01380.1730.00040.00080.1704-0.0050.177521.0125-14.1815-42.283
120.1065-0.2113-0.1110.41930.22020.11560.0034-0.08170.12840.0368-0.0340.1387-0.1185-0.10260.03050.2204-0.0003-0.00030.22050.00140.21847.6527-9.3986-52.6472
131.0224-0.10080.05770.68760.17930.8822-0.0280.07620.0451-0.07080.04760.01630.0131-0.046-0.01950.1150.0107-0.00670.1191-0.01010.114611.8252-27.751-39.8725
140.2358-0.3574-0.16430.54170.2490.1144-0.00760.0867-0.1773-0.0623-0.0062-0.05660.14310.08550.01390.2139-0.0007-0.00070.21420.00170.21072.8756-54.6271-34.9258
150.272-0.00680.52591.83850.58211.60530.0146-0.0159-0.0798-0.0104-0.02290.02950.0911-0.04180.00840.12920.00630.00010.1210.00480.117413.0389-38.6233-34.6194
160.1190.20340.01520.34750.0260.002-0.01210.050.0545-0.03840.006-0.0315-0.06250.06640.00620.16390.00210.00130.1665-0.00060.165920.5588-32.4377-43.8404
170.44020.45630.12160.6646-0.14050.580200.0936-0.1012-0.04610.00190.1230.1002-0.1126-0.00190.12740.0020.00120.1234-0.00210.12325.0681-35.153-42.5668
180.31740.1028-0.13630.3361-0.27920.241-0.01950.02130.0282-0.04450.01820.0114-0.02250.00950.00140.15590.00280.00020.159-0.00030.15594.5368-19.0958-44.1017
190000000.0147-0.04380.01120.1007-0.0463-0.1093-0.08360.10280.03150.2096000.209600.209615.4238-15.1513-29.5148
200.09690.2804-0.08610.8114-0.24920.07650.01930.07220.1506-0.0229-0.0183-0.0536-0.15810.1246-0.00110.19660.001900.2012-0.00040.200513.8135-13.3429-29.0952
210.99720.62750.39331.394-0.05511.48450.01760.04210.0364-0.0499-0.01770.028-0.0452-0.042800.1532-0.0032-0.00030.14960.00240.145419.3274-45.3723-68.4227
220.23840.02820.08270.41160.09370.3641-0.00050.0612-0.1017-0.0659-0.0021-0.00780.12770.02710.00260.203-0.00020.00080.21010.00080.212315.0881-56.6799-59.3049
230.3459-0.4188-0.38470.5070.46580.4279-0.0124-0.0386-0.00270.06030.01280.03080.0217-0.0162-0.00040.2563-0.0008-0.00160.25750.00090.256724.7335-69.484-68.5373
240.41050.2172-0.07130.115-0.03770.01240.0356-0.0798-0.02440.0523-0.02760.01990.0372-0.0329-0.00810.22110.0048-0.00050.21490.00040.22235.3966-68.1355-51.3004
250.31920.19760.0620.20110.11370.084-0.01620.08090.1053-0.03670.0062-0.0682-0.09980.10290.010.20790.00160.00090.2075-0.00030.208156.4319-50.527-65.0289
260.9389-0.31980.24210.54740.1650.9844-0.0076-0.0858-0.11050.0361-0.0039-0.00140.1088-0.02930.01160.17350.0018-0.00040.1799-0.00590.176447.1706-64.1038-58.5885
270.4550.10970.30220.12660.08860.38280.01270.0571-0.0167-0.07930.00580.0975-0.0099-0.0822-0.01850.2264-0.00120.00350.22020.00180.222642.2969-65.6605-69.2047
280000000.00420.15940.0807-0.1516-0.01010.0543-0.0602-0.03020.00580.3156000.315600.315636.2659-70.8493-80.7462
290.15570.0769-0.02110.2319-0.02290.28480.0033-0.0935-0.02660.0911-0.0011-0.0320.02410.0226-0.00220.29280.00150.0010.2923-0.0010.295141.3051-80.5146-55.717
300.0093-0.0367-0.07040.1450.27820.5339-0.00350.0385-0.31410.0107-0.00920.10610.3193-0.13440.01260.20670.0004-0.00050.20790.00070.208735.0519-74.2797-59.1359
311.6817-0.68210.03190.28040.07041.8843-0.00990.0266-0.0615-0.02940.0116-0.02220.05040.0143-0.00180.10340.00240.0010.12730.00150.103940.1255-56.7006-60.6023
320.30120.1-0.15330.51990.17550.396-0.0117-0.1289-0.07820.1579-0.0058-0.15820.09190.14280.01750.1936-0.0040.00510.1973-0.00230.198849.0706-42.2701-51.0304
330.10140.10690.18481.41350.82730.64430.00950.0654-0.2747-0.048-0.0027-0.13320.28990.1621-0.00690.215200.00060.21780.00250.215547.4148-52.9312-40.397
340.8233-0.14510.02470.8988-0.00320.96950.0467-0.074-0.00610.0861-0.0308-0.06390.02710.007-0.0160.11890.00970.01070.11470.00670.111933.122-48.8452-54.9127
350.62-0.6348-0.32320.64990.33090.1685-0.0262-0.12990.04870.18940.02210.1473-0.0745-0.11160.00410.2177-0.0016-0.00230.21860.00090.21455.7661-57.7306-58.583
361.4285-0.2965-0.34430.543-0.19591.6191-0.0088-0.00450.0227-0.02640.00690.09770.0169-0.07270.00180.11410.0096-0.00360.12470.00190.110921.59-48.6445-60.3327
370.74990.1922-0.00960.22940.08070.03850.0006-0.02880.00420.0344-0.0047-0.0227-0.02230.01790.0040.17920.00220.00050.1735-0.00180.177928.9604-39.5836-51.1876
380.2682-0.04350.12650.41760.0070.29970.0011-0.0264-0.03310.013-0.0008-0.02190.00790.0191-0.00020.16120.00120.00080.1546-0.00060.148834.9563-55.7367-51.0367
390.06070.02580.09640.01530.03140.1742-0.01770.0530.0376-0.0220.0062-0.0086-0.04190.0480.01160.20680.00130.00070.2058-0.00030.207946.0629-45.3401-65.445
400.46690.0083-0.03620.0665-0.07130.233-0.0149-0.00120.03210.04380.0178-0.1102-0.08810.1108-0.00290.19930.00410.00130.19030.00020.196846.7335-47.8859-65.9465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 68
2X-RAY DIFFRACTION2A69 - 82
3X-RAY DIFFRACTION3A83 - 107
4X-RAY DIFFRACTION4A108 - 120
5X-RAY DIFFRACTION5A121 - 153
6X-RAY DIFFRACTION6A154 - 194
7X-RAY DIFFRACTION7A195 - 224
8X-RAY DIFFRACTION8A225 - 251
9X-RAY DIFFRACTION9A252 - 290
10X-RAY DIFFRACTION10A291 - 315
11X-RAY DIFFRACTION11A316 - 335
12X-RAY DIFFRACTION12A336 - 349
13X-RAY DIFFRACTION13A350 - 372
14X-RAY DIFFRACTION14A373 - 390
15X-RAY DIFFRACTION15A391 - 402
16X-RAY DIFFRACTION16A403 - 425
17X-RAY DIFFRACTION17A426 - 435
18X-RAY DIFFRACTION18A436 - 454
19X-RAY DIFFRACTION19A455 - 474
20X-RAY DIFFRACTION20A475 - 489
21X-RAY DIFFRACTION21B59 - 71
22X-RAY DIFFRACTION22B72 - 107
23X-RAY DIFFRACTION23B108 - 117
24X-RAY DIFFRACTION24B118 - 164
25X-RAY DIFFRACTION25B165 - 182
26X-RAY DIFFRACTION26B183 - 198
27X-RAY DIFFRACTION27B199 - 228
28X-RAY DIFFRACTION28B236 - 246
29X-RAY DIFFRACTION29B247 - 290
30X-RAY DIFFRACTION30B291 - 299
31X-RAY DIFFRACTION31B300 - 315
32X-RAY DIFFRACTION32B316 - 341
33X-RAY DIFFRACTION33B342 - 349
34X-RAY DIFFRACTION34B350 - 372
35X-RAY DIFFRACTION35B373 - 389
36X-RAY DIFFRACTION36B390 - 402
37X-RAY DIFFRACTION37B403 - 424
38X-RAY DIFFRACTION38B425 - 454
39X-RAY DIFFRACTION39B455 - 473
40X-RAY DIFFRACTION40B474 - 489

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