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- PDB-3dgh: Crystal Structure of Drosophila Thioredoxin Reductase, C-terminal... -

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Basic information

Entry
Database: PDB / ID: 3dgh
TitleCrystal Structure of Drosophila Thioredoxin Reductase, C-terminal 8-residue truncation
ComponentsThioredoxin reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE / rossmann / flavoprotein / Alternative initiation / FAD / Mitochondrion / NADP / Redox-active center / Transit peptide
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / antioxidant activity / cell redox homeostasis / determination of adult lifespan / flavin adenine dinucleotide binding / protein homodimerization activity / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase 1, mitochondrial
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.745 Å
AuthorsEckenroth, B.E. / Hondal, R.J. / Everse, S.J.
CitationJournal: To be Published
Title: Crystal Structure of Drosophila Thioredoxin Reductase, C-terminal 8-residue truncation
Authors: Eckenroth, B.E. / Hondal, R.J. / Everse, S.J.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase 1, mitochondrial
B: Thioredoxin reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0338
Polymers105,0782
Non-polymers1,9556
Water11,602644
1
A: Thioredoxin reductase 1, mitochondrial
B: Thioredoxin reductase 1, mitochondrial
hetero molecules

A: Thioredoxin reductase 1, mitochondrial
B: Thioredoxin reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,06616
Polymers210,1564
Non-polymers3,91112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area24430 Å2
ΔGint-246 kcal/mol
Surface area70130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-119 kcal/mol
Surface area36940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.755, 135.755, 132.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin reductase 1, mitochondrial / TrxR-1


Mass: 52538.883 Da / Num. of mol.: 2 / Fragment: UNP residues 112-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Trxr-1, GR, CG2151 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: P91938, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Succinate, 1.0 M Li2SO4, 0.6 M (NH4)2SO4, pH 5.5, vapor diffusion, hanging drop, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2008 / Details: mirrors
RadiationMonochromator: DCM pair, flat Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.745→32 Å / Num. obs: 125246 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.085 / Χ2: 1.234 / Net I/σ(I): 11.6
Reflection shellResolution: 1.745→1.81 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.02 / Num. unique all: 12401 / Χ2: 1.142 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å11.97 Å
Translation2.25 Å11.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.745→29.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.855 / SU B: 3.932 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 12558 10 %RANDOM
Rwork0.2 ---
obs0.203 125158 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 35.02 Å2 / Biso mean: 6.957 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.745→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 126 644 8058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227568
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.98910297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11124.11309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.851151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0821542
X-RAY DIFFRACTIONr_chiral_restr0.1160.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025628
X-RAY DIFFRACTIONr_nbd_refined0.2140.23524
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2468
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.214
X-RAY DIFFRACTIONr_mcbond_it0.5981.54842
X-RAY DIFFRACTIONr_mcangle_it0.97527555
X-RAY DIFFRACTIONr_scbond_it1.77433212
X-RAY DIFFRACTIONr_scangle_it2.7014.52742
LS refinement shellResolution: 1.745→1.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 899 -
Rwork0.236 8133 -
all-9032 -
obs--98.52 %
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)
11.42881.14120.42024.6254-1.05081.8242-0.0779-0.0675-0.0480.1302-0.0102-0.1518-0.37530.06180.08810.0585-0.0466-0.0076-0.0546-0.0085-0.01846.61640.325-12.93
22.76550.87162.82881.2951-0.10393.8647-0.01950.00030.00740.13830.02330.0641-0.5619-0.0157-0.00390.088-0.03460.0106-0.0783-0.0116-0.022342.86738.714-11.32
30.57390.2709-0.40781.0161-0.41960.7859-0.0283-0.07950.0324-0.1609-0.0267-0.06040.0627-0.03220.05510.0104-0.00040.0144-0.0384-0.0024-0.004731.94624.611-20.814
40.60880.6199-0.49841.6482-0.78390.7391-0.03060.01880.0239-0.0944-0.025-0.03160.1184-0.11060.05550.0279-0.03470.0173-0.0295-0.0137-0.013621.1111.287-10.658
50.80441.54850.51493.59381.29930.82390.0084-0.01150.0042-0.0687-0.0001-0.07550.0241-0.0502-0.0083-0.0241-0.00540.014-0.01920.00030.002522.57421.037-15.032
61.5790.9956-1.03590.9877-0.60991.1352-0.0322-0.04970.11110.0161-0.03750.0089-0.33880.01190.06980.0577-0.00430.0243-0.0832-0.0018-0.015340.9643.226-17.879
70.2303-0.1538-0.31380.3989-0.32551.39360.060.0384-0.03230.0359-0.1291-0.1246-0.210.12210.06910.0281-0.0501-0.0078-0.04740.0120.017946.8239.064-19.627
81.6744-0.4604-0.55090.98750.51411.3539-0.0244-0.02630.0375-0.16420.01570.00260.0164-0.02720.00870.0317-0.00280.0049-0.0460.0036-0.030731.97820.12-33.205
90.8762-0.2834-0.40450.36760.03690.79770.01790.02940.0325-0.0479-0.0323-0.04330.1493-0.01860.01440.0296-0.00490.016-0.0433-0.0032-0.010832.2279.837-26.285
101.2532-0.4463-0.43440.9150.01011.4978-0.00290.07750.0215-0.1927-0.0302-0.01510.1246-0.00610.03320.030.00580.0379-0.0511-0.0139-0.036134.7256.196-29.33
112.71990.43740.74560.29950.14951.0325-0.03370.0531-0.0804-0.1064-0.0384-0.09030.14810.04990.07220.04880.03050.045-0.06130.0059-0.003141.3090.826-22.894
122.509-1.9140.3283.6361-1.18832.3155-0.00980.1192-0.1456-0.43830.02720.05860.2273-0.1877-0.01750.0682-0.0076-0.0065-0.0468-0.0295-0.100432.15910.075-41.219
130.08690.25910.161.40340.40681.15660.0441-0.00290.0046-0.2054-0.0253-0.16570.13370.0414-0.01890.06760.02530.0366-0.0505-0.0097-0.03637.39711.849-37.895
140.85750.1297-0.14471.707-0.54291.8372-0.0355-0.0052-0.1022-0.0152-0.0549-0.38330.00220.22630.0905-0.0844-0.02620.0241-0.02270.01240.048753.51729.728-19.833
150.72280.85140.71610.41781.26322.19020.1189-0.0654-0.16130.5687-0.3421-0.9289-0.08550.2310.2233-0.0533-0.0677-0.0695-0.02690.06260.049154.7227.38-6.234
161.164-0.21280.40310.288-0.02310.6041-0.07860.0258-0.0045-0.0839-0.0059-0.06080.09760.10520.0845-0.01420.04430.0376-0.02480.02110.022152.6552.319-13.751
176.42610.67311.12480.3905-0.17490.56350.0213-0.0765-0.0294-0.008-0.0686-0.05010.19940.02520.04730.09520.00690.0331-0.1068-0.0003-0.033133.218-7.962-8.614
182.23630.53080.69280.53140.16250.6069-0.02060.00010.0279-0.0462-0.0232-0.09920.21780.13680.0439-0.00840.07190.0327-0.0070.03340.009553.318-1.369-8.706
190.66830.1724-0.01170.1923-0.16661.0197-0.0434-0.01420.021-0.0218-0.0064-0.0350.17960.09750.04970.01540.0450.0177-0.03430.00910.000246.5441.894-0.844
206.1384-1.3249-8.5343.89871.029212.0474-0.2901-0.45380.2160.25560.1762-0.44310.76070.36420.11380.0480.1088-0.0152-0.00970.00690.022654.258-11.1-6.586
210.55551.2681-0.59093.2236-0.63712.1710.0699-0.0360.0066-0.0005-0.123-0.22940.02220.01470.053-0.0164-0.01540.0169-0.04250.01370.033740.80825.515-18.793
223.11530.0932-0.57481.7075-0.00761.9084-0.2081-0.103-0.3645-0.04090.0081-0.1720.64560.16890.19990.28290.19080.1126-0.13160.09240.008547.456-25.79811.771
231.5113-0.225-0.11631.3657-0.30450.8776-0.1062-0.05-0.07150.0580.0051-0.01590.32270.04230.1010.2019-0.01720.0519-0.10050.0139-0.063127.388-16.86411.597
240.4067-0.42150.41851.2198-0.75231.6048-0.0848-0.0310.02690.09690.00720.05630.0996-0.21850.07770.0096-0.04580.0254-0.0134-0.0171-0.016217.6934.007-5.888
2513.8569-9.1646-1.22087.03310.39370.8162-0.16670.0576-0.46660.30530.08810.340.4219-0.1290.07870.1727-0.0650.0368-0.1136-0.0079-0.063624.277-17.0460.382
261.90190.2734-4.31137.1378-0.202115.02820.0853-0.3468-0.75290.1376-0.4483-0.95130.28940.39050.3630.21230.05910.0588-0.15180.08810.105541.349-30.94315.577
271.46380.169-0.00190.2102-0.21340.2384-0.0526-0.0955-0.12530.0736-0.00280.04750.4223-0.04640.05530.1472-0.01670.0565-0.05070.0426-0.070725.01-13.73720.747
289.04-8.426917.043523.113300-0.23160.0745-0.76181.0134-0.33481.14990.5117-0.36590.56630.0187-0.09140.1066-0.05370.0120.002611.962-8.48510.719
291.4541-0.3890.36030.5530.1951.54140.01070.0137-0.0680.0309-0.00280.00160.2622-0.076-0.0080.0691-0.03170.0428-0.05290.0084-0.031720.402-0.57912.042
301.46170.2581-0.08060.0759-0.05580.90160.0289-0.08360.06930.1124-0.02920.00050.0798-0.03430.00030.0524-0.00060.0338-0.0305-0.0089-0.039124.9288.23917.369
313.57522.89480.08015.0784-0.16552.46910.0259-0.03670.05580.3010.08290.2370.2293-0.3178-0.10890.0601-0.06630.1153-0.00150.0219-0.10710.923-3.37125.578
324.97993.15133.16685.84154.92168.02530.2361-0.28930.20450.3189-0.1570.256-0.0949-0.3988-0.0790.0799-0.05850.1416-0.01380.0148-0.095211.1581.69827.823
333.671-2.13130.6651.2478-0.43560.3551-0.037-0.4067-0.2110.10540.10550.19580.3194-0.123-0.06850.18790.00640.0487-0.02990.0616-0.069827.328-12.85522.802
344.1839-0.3111-0.042.7425-1.28163.1663-0.1707-0.0577-0.30030.29550.0334-0.09650.29920.05760.13720.1620.1159-0.0051-0.01160.0472-0.067645.332-15.64528.173
351.8266-0.7587-0.01682.2017-1.08971.8041-0.1353-0.17710.00710.0521-0.0712-0.25310.26430.16560.20660.08080.10450.0044-0.03390.0694-0.031249.561-11.82316.117
361.90481.07330.67281.1830.46910.8159-0.0224-0.13-0.13850.24280.032-0.01450.13130.0032-0.00970.05130.0349-0.0115-0.0337-0.0024-0.033637.7678.37214.234
372.7592-0.39642.13910.6408-0.08693.0699-0.2118-0.01830.3743-0.04180.0567-0.1204-0.15850.15010.155-0.03910.0006-0.0284-0.0192-0.03730.02942.13420.42613.243
381.4369-0.50850.84640.4338-0.21680.9522-0.01010.04110.08630.0230.0086-0.07060.01510.07170.0016-0.0215-0.0082-0.0027-0.0107-0.011-0.001535.84217.6345.517
391.18580.04310.02810.3655-0.19450.5218-0.0513-0.04330.0563-0.0121-0.0142-0.05530.09240.05920.0656-0.0060.0265-0.0108-0.02190.0008-0.003644.2829.6386.088
400.4694-0.0888-0.13070.1637-0.45451.5989-0.0643-0.03920.060.0170.02120.0111-0.04090.00630.0432-0.01430.0096-0.0052-0.02830.00290.015343.44516.596-2.303
410.1061-0.3701-0.90893.12520.780110.90560.11010.10410.18220.0250.3071-0.2116-0.20180.0817-0.4173-0.05910.0045-0.0159-0.0493-0.02050.084241.90224.359.232
422.9804-5.11971.47758.8793-2.26181.6339-0.11880.03230.0395-0.00230.0830.28360.3943-0.03280.03580.18180.03950.0515-0.0710.0337-0.027935.073-13.55414.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 251 - 19
2X-RAY DIFFRACTION2AA26 - 4220 - 36
3X-RAY DIFFRACTION3AA43 - 6737 - 61
4X-RAY DIFFRACTION4AA68 - 8962 - 83
5X-RAY DIFFRACTION5AA90 - 11684 - 110
6X-RAY DIFFRACTION6AA117 - 146111 - 140
7X-RAY DIFFRACTION7AA147 - 162141 - 156
8X-RAY DIFFRACTION8AA163 - 185157 - 179
9X-RAY DIFFRACTION9AA186 - 207180 - 201
10X-RAY DIFFRACTION10AA208 - 221202 - 215
11X-RAY DIFFRACTION11AA222 - 244216 - 238
12X-RAY DIFFRACTION12AA245 - 260239 - 254
13X-RAY DIFFRACTION13AA261 - 292255 - 286
14X-RAY DIFFRACTION14AA293 - 342287 - 336
15X-RAY DIFFRACTION15AA343 - 363337 - 357
16X-RAY DIFFRACTION16AA364 - 395358 - 389
17X-RAY DIFFRACTION17AA396 - 410390 - 404
18X-RAY DIFFRACTION18AA411 - 432405 - 426
19X-RAY DIFFRACTION19AA433 - 472427 - 466
20X-RAY DIFFRACTION20AA473 - 483467 - 477
21X-RAY DIFFRACTION21AC500
22X-RAY DIFFRACTION22BB7 - 391 - 33
23X-RAY DIFFRACTION23BB40 - 6634 - 60
24X-RAY DIFFRACTION24BB67 - 9461 - 88
25X-RAY DIFFRACTION25BB95 - 11589 - 109
26X-RAY DIFFRACTION26BB116 - 153110 - 147
27X-RAY DIFFRACTION27BB154 - 182148 - 176
28X-RAY DIFFRACTION28BB183 - 190177 - 184
29X-RAY DIFFRACTION29BB191 - 212185 - 206
30X-RAY DIFFRACTION30BB213 - 245207 - 239
31X-RAY DIFFRACTION31BB246 - 259240 - 253
32X-RAY DIFFRACTION32BB260 - 278254 - 272
33X-RAY DIFFRACTION33BB279 - 295273 - 289
34X-RAY DIFFRACTION34BB296 - 313290 - 307
35X-RAY DIFFRACTION35BB314 - 363308 - 357
36X-RAY DIFFRACTION36BB364 - 385358 - 379
37X-RAY DIFFRACTION37BB386 - 399380 - 393
38X-RAY DIFFRACTION38BB400 - 426394 - 420
39X-RAY DIFFRACTION39BB427 - 455421 - 449
40X-RAY DIFFRACTION40BB456 - 472450 - 466
41X-RAY DIFFRACTION41BB473 - 479467 - 473
42X-RAY DIFFRACTION42BF500

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