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- PDB-5ebk: Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlo... -

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Basic information

Entry
Database: PDB / ID: 5ebk
TitleTrypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine
ComponentsTrypanothione reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Trypanothione reductase / : / 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 ...Trypanothione reductase / : / 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 / Chem-RDS / Trypanothione reductase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsIlari, A. / Angiulli, G.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2017
Title: Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives.
Authors: Saccoliti, F. / Angiulli, G. / Pupo, G. / Pescatori, L. / Madia, V.N. / Messore, A. / Colotti, G. / Fiorillo, A. / Scipione, L. / Gramiccia, M. / Di Muccio, T. / Di Santo, R. / Costi, R. / Ilari, A.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Jan 10, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Oct 23, 2024Group: Structure summary / Category: 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: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,35112
Polymers110,5152
Non-polymers3,83610
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.500, 102.500, 192.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 10 - 480 / Label seq-ID: 30 - 500

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.000465, -0.999998, -0.001705), (-0.999995, -0.000471, 0.003282), (-0.003283, 0.001703, -0.999993)51.16506, 51.23015, -0.0418

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Components

#1: Protein Trypanothione reductase


Mass: 55257.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sandfly / Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: TRYR, LINJ_05_0350 / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A4HSF7, trypanothione-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-RDS / 6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine


Mass: 309.814 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H16ClN3OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density meas: 2017200 Mg/m3 / Density % sol: 73.2 % / Description: Small diamond-shaped yellow crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulphate, Lithium sulphate, Tris HCl / PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.543
11-H, K, -L20.457
ReflectionResolution: 3.51→48.15 Å / Num. all: 24914 / Num. obs: 127631 / % possible obs: 99.6 % / Redundancy: 5.12 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.16
Reflection shellResolution: 3.51→3.72 Å / Redundancy: 5.04 % / Mean I/σ(I) obs: 1.72 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MxCuBEdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jk6
Resolution: 3.51→48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.926 / SU B: 40.928 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23324 1261 5.1 %RANDOM
Rwork0.20821 ---
obs0.20951 23650 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.04 Å2
Baniso -1Baniso -2Baniso -3
1--8.95 Å2-0 Å2-0 Å2
2---8.95 Å2-0 Å2
3---17.91 Å2
Refinement stepCycle: 1 / Resolution: 3.51→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7366 0 251 0 7617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197783
X-RAY DIFFRACTIONr_bond_other_d0.0020.027278
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.94710553
X-RAY DIFFRACTIONr_angle_other_deg1.0612.9716753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64224.331314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.447151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7161538
X-RAY DIFFRACTIONr_chiral_restr0.0740.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028762
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021750
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5725.6873897
X-RAY DIFFRACTIONr_mcbond_other1.5575.6813893
X-RAY DIFFRACTIONr_mcangle_it2.6968.514859
X-RAY DIFFRACTIONr_mcangle_other2.6958.514860
X-RAY DIFFRACTIONr_scbond_it1.7216.2643886
X-RAY DIFFRACTIONr_scbond_other1.7076.2613883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9939.3245689
X-RAY DIFFRACTIONr_long_range_B_refined8.52750.2358713
X-RAY DIFFRACTIONr_long_range_B_other8.52750.2438714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
4224loose positional0.025
2758tight thermal6.420.5
4224loose thermal6.810
LS refinement shellResolution: 3.499→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 95 -
Rwork0.365 1666 -
obs--95.09 %
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)
14.00824.9438-0.44078.87442.80634.24210.27680.04550.4060.2736-0.16150.2469-0.1789-0.3591-0.11530.52670.0906-0.00520.69260.15610.5144-12.624625.812721.0391
22.4858-0.8854-4.33550.40371.60827.6291-0.1270.26130.09560.15270.15170.05760.408-0.3426-0.02470.63150.04770.03160.69640.13590.50532.903415.58919.2076
310.417110.7071-2.123911.2744-3.11494.2134-0.65220.4507-0.7866-0.96250.4129-0.80720.88820.37340.23920.59830.14150.07570.5933-0.02740.424827.453518.8203-2.5261
48.6905-8.0231-9.55813.08579.7317.3307-0.3302-0.6897-0.03710.56450.4723-0.39570.63770.3168-0.14210.5658-0.02390.01610.4740.04490.48838.831416.136115.6913
55.98860.02050.13213.7142-0.38954.96820.14980.13650.1926-0.04160.01830.01180.3751-0.1461-0.16810.53790.01980.0210.63210.13720.1955-12.347515.654820.3322
64.29933.4921-1.157313.3148-1.89366.1896-0.1510.12490.2146-0.23660.19450.64920.5054-0.1294-0.04350.41810.0321-0.07560.71130.09770.2676-17.124812.481616.39
71.8975-3.16191.10965.3182-1.55335.1153-0.0277-0.0209-0.01040.128-0.0373-0.05880.3348-0.48120.06510.7236-0.07770.04330.68660.00460.29743.29568.0988-4.4683
86.047-4.69042.06445.8738-2.07715.7462-0.33590.27630.0233-0.39360.2358-0.29770.0379-0.46640.10010.59370.00690.04650.5676-0.02540.26448.853619.604-12.6663
93.36621.5184-1.582611.0262-2.35411.05830.31260.5121-0.3964-0.1936-0.4128-0.08070.0809-0.13410.10030.8732-0.1014-0.01190.7643-0.10080.40096.70459.909-16.973
102.0764-0.35890.49751.94143.34256.5350.1658-0.1209-0.95880.10240.13740.19580.492-0.0068-0.30330.8882-0.19880.00410.5020.12260.69474.15344.4365-11.882
114.4898-1.8958-2.064810.6109-6.58487.10430.16250.9456-0.337-0.3888-0.04531.07890.3096-0.5887-0.11710.4346-0.007-0.03740.97110.10330.5409-20.519320.06433.9037
126.69030.48710.14980.1914-0.63482.76030.1830.16090.9955-0.05050.06530.15850.0807-0.0702-0.24830.66940.0779-0.03190.88320.25740.6107-12.917228.23647.6139
132.3021-0.3711-3.39680.331-0.30068.07660.43980.13810.0432-0.12420.03120.266-0.4937-0.3724-0.4710.5178-0.0201-0.05220.5409-0.03360.7672-2.889833.8596-0.2079
1416.07884.64810.53383.1518-1.81383.0443-0.56950.21810.1008-0.1360.44860.5381-0.3354-0.39380.12090.59140.1114-0.11730.71380.04090.6874-3.442441.5596-18.1029
1526.3088-14.572715.05718.4605-8.137112.0926-0.40480.22160.9408-0.21940.2588-0.5733-0.80350.0910.14590.7986-0.14650.08330.68370.0490.571424.609333.9325-12.9949
1615.7848-14.11172.167916.32070.19643.0913-0.188-0.04660.3473-0.24450.2350.0432-0.0778-0.3482-0.0470.5865-0.0327-0.00470.56770.09240.52416.576540.559-14.4629
179.32260.6703-1.02199.392.2825.1392-0.07990.30190.29780.2272-0.1380.6478-0.49840.03890.21790.44930.04420.02320.52030.04340.51455.671339.009-5.056
1816.28152.1923-2.76217.05795.831625.7438-0.2036-0.49941.114-0.08450.8741.2342-0.4135-2.3407-0.67040.49180.2368-0.00750.79440.23350.823-0.917648.831-4.7597
1912.30313.03177.78250.7721.95475.01520.04130.40760.24-0.11390.0020.0206-0.18790.1844-0.04330.93640.11740.14760.66710.1370.582213.530348.3348-7.2348
208.7242-2.9513-0.76145.3841-1.6870.93060.36290.29330.0233-0.5014-0.21690.33140.10470.0076-0.14590.62130.092-0.15640.8160.10410.44711.021245.2093-24.0595
213.53260.51894.23465.1015-1.76826.22430.0704-0.6888-0.05660.3111-0.0929-0.2216-0.118-0.78320.02250.66970.10850.2230.62590.06450.424326.153362.8888-19.7319
227.4583-4.40555.09828.39990.89396.124-0.8852-0.5991-0.25770.69991.02120.2466-0.55580.0658-0.1360.6183-0.07670.23920.71140.15830.385532.611257.9988-19.0133
230.5340.2423-1.08098.1308-7.7398.77430.2464-0.0276-0.068-0.3978-0.11060.311-0.15550.1505-0.13590.57130.03810.01740.64890.03930.618432.824942.0559-4.7174
2410.74175.95593.643812.1039-1.07982.54570.48460.19480.06990.7984-0.6054-1.03770.13270.43660.12080.66420.0978-0.04240.76590.10840.726728.758518.28734.8388
2512.98733.4540.34352.33414.288512.46450.1565-0.9421-1.38090.496-0.1024-0.39661.34930.4604-0.05410.53290.0831-0.0090.73210.16440.716540.516730.0074-2.4781
264.6684-5.67328.688912.2795-14.717719.43280.0150.235-0.1399-0.8057-0.2502-0.54710.52260.3760.23520.53160.00180.05430.55030.01110.403333.09545.6328-19.1981
273.3249-1.2045-0.39946.8278-0.01594.18770.0206-0.11750.14740.23620.1361-0.0145-0.14380.5689-0.15680.6881-0.04280.13890.58030.00530.303437.400166.5763-18.979
2813.12632.3811-2.05324.2175-2.46986.9265-0.1551-0.19591.1110.4266-0.1503-0.2444-0.09090.64180.30540.7838-0.01380.02960.3932-0.11560.352441.074269.1393-18.0184
290.0271-0.17320.30512.0786-2.94536.8430.07190.06510.06050.2094-0.083-0.2641-0.47491.01620.01110.869-0.12530.04890.88320.16240.5941.760655.63011.3287
301.91140.99511.41755.73676.2067.21210.2361-0.00070.0888-0.3503-0.2014-0.2582-0.58850.1888-0.03470.60610.11730.03250.76890.22290.382439.016540.51834.7863
317.0345-1.40590.46361.2396-1.33263.7752-0.0019-0.3098-0.26110.1430.03520.4285-0.23410.0449-0.03320.5831-0.01950.01850.58740.01870.262330.043242.873915.4759
321.5757-1.2226-0.08624.47931.63233.69920.2195-0.2198-0.01330.34390.1873-0.5767-0.38150.9127-0.40690.5825-0.1114-0.09080.79290.05170.35745.754547.074913.4869
338.2398-2.8749-1.17955.5093-1.3968.27340.1155-0.57740.75371.1994-0.3103-0.3811-1.19010.63490.19480.8968-0.0562-0.00310.3243-0.1040.396332.124471.5743-3.4755
340.22410.84170.55623.74192.63612.02140.0538-0.05120.164-0.0920.16670.1906-0.1373-0.0363-0.22060.9432-0.00140.18590.80940.12410.832423.083664.7654-7.6687
350.22821.0382-0.46255.4166-0.465.86790.24890.06020.21440.94250.12711.0793-0.70990.3591-0.3760.55850.13460.21560.83780.03750.901215.970858.7531-4.4405
362.21630.5592-0.3785.62840.01154.07880.1052-0.5640.8494-0.04070.31350.088-0.5090.1385-0.41870.63110.0211-0.01380.4873-0.06150.526815.668752.223313.2279
377.9154-8.4404-1.112415.4021.21221.70570.0302-0.21370.04570.3848-0.23140.4652-0.1422-0.18770.20120.4990.04780.03420.594-0.06580.402811.871240.608813.9817
382.52260.4793-1.70884.0040.59965.93760.04890.79310.8365-0.1207-0.06410.2081-0.2672-0.71070.01520.6270.20950.04540.4810.05350.61999.226945.78383.9701
395.33335.21417.199110.27495.594810.1597-0.2136-0.6540.11190.66010.20210.7371-0.3617-1.06550.01160.78310.05130.27330.81140.05010.57763.582236.2857.4799
407.0895-1.5935-3.223713.3325-1.06781.72030.2075-0.64420.4750.66360.0160.333-0.18630.2556-0.22350.63480.15230.0850.7759-0.20140.56115.428751.06824.9852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 67
3X-RAY DIFFRACTION3A68 - 95
4X-RAY DIFFRACTION4A96 - 111
5X-RAY DIFFRACTION5A112 - 139
6X-RAY DIFFRACTION6A140 - 160
7X-RAY DIFFRACTION7A161 - 198
8X-RAY DIFFRACTION8A199 - 242
9X-RAY DIFFRACTION9A243 - 260
10X-RAY DIFFRACTION10A261 - 290
11X-RAY DIFFRACTION11A291 - 317
12X-RAY DIFFRACTION12A318 - 349
13X-RAY DIFFRACTION13A350 - 378
14X-RAY DIFFRACTION14A379 - 394
15X-RAY DIFFRACTION15A395 - 407
16X-RAY DIFFRACTION16A408 - 422
17X-RAY DIFFRACTION17A423 - 445
18X-RAY DIFFRACTION18A446 - 451
19X-RAY DIFFRACTION19A452 - 470
20X-RAY DIFFRACTION20A471 - 486
21X-RAY DIFFRACTION21B2 - 26
22X-RAY DIFFRACTION22B27 - 42
23X-RAY DIFFRACTION23B43 - 72
24X-RAY DIFFRACTION24B73 - 86
25X-RAY DIFFRACTION25B87 - 96
26X-RAY DIFFRACTION26B97 - 117
27X-RAY DIFFRACTION27B118 - 139
28X-RAY DIFFRACTION28B140 - 155
29X-RAY DIFFRACTION29B156 - 181
30X-RAY DIFFRACTION30B182 - 211
31X-RAY DIFFRACTION31B212 - 246
32X-RAY DIFFRACTION32B247 - 290
33X-RAY DIFFRACTION33B291 - 314
34X-RAY DIFFRACTION34B315 - 349
35X-RAY DIFFRACTION35B350 - 367
36X-RAY DIFFRACTION36B368 - 387
37X-RAY DIFFRACTION37B388 - 428
38X-RAY DIFFRACTION38B429 - 454
39X-RAY DIFFRACTION39B455 - 471
40X-RAY DIFFRACTION40B472 - 488

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