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- PDB-2x4h: Crystal Structure of the hypothetical protein SSo2273 from Sulfol... -

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Basic information

Entry
Database: PDB / ID: 2x4h
TitleCrystal Structure of the hypothetical protein SSo2273 from Sulfolobus solfataricus
ComponentsHYPOTHETICAL PROTEIN SSO2273Hypothesis
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionJan 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN SSO2273
B: HYPOTHETICAL PROTEIN SSO2273
C: HYPOTHETICAL PROTEIN SSO2273
D: HYPOTHETICAL PROTEIN SSO2273
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,74918
Polymers63,8334
Non-polymers91614
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-562 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.100, 72.100, 260.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A10 - 26
2114B10 - 26
3114C10 - 26
4114D10 - 26
1214A33 - 40
2214B33 - 40
3214C33 - 40
4214D33 - 40
1314A44 - 57
2314B44 - 57
3314C44 - 57
4314D44 - 57
1414A60 - 62
2414B60 - 62
3414C60 - 62
4414D60 - 62
1514A67 - 69
2514B67 - 69
3514C67 - 69
4514D67 - 69
1614A71 - 93
2614B71 - 93
3614C71 - 93
4614D71 - 93
1714A98 - 110
2714B98 - 110
3714C98 - 110
4714D98 - 110
1814A115 - 124
2814B115 - 124
3814C115 - 124
4814D115 - 124

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Components

#1: Protein
HYPOTHETICAL PROTEIN SSO2273 / Hypothesis


Mass: 15958.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97WF3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: OFFLINE FUJI PLATE.
Crystal growpH: 7
Details: 5.6%-6.8% PEG 1000, 80MM ZN ACETATE AND 0.1M MES PH7. THE CRYSTALS WERE CRYOPROTECTED BY ADDITION OF 25% PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: FUJIFILM / Detector: IMAGE PLATE / Date: Mar 27, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 2.3→28.89 Å / Num. obs: 30005 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→28.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.785 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ONE TO NINE ARE DISORDERED IN CHAINS A AND D AND RESIDUES ONE TO EIGHT ARE DISORDERED IN CHAINS B AND C. ATOM RECORD CONTAINS SUM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ONE TO NINE ARE DISORDERED IN CHAINS A AND D AND RESIDUES ONE TO EIGHT ARE DISORDERED IN CHAINS B AND C. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24625 1577 5 %RANDOM
Rwork0.20218 ---
obs0.20438 30005 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 14 78 4287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224275
X-RAY DIFFRACTIONr_bond_other_d0.0010.022999
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9835766
X-RAY DIFFRACTIONr_angle_other_deg0.8837341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6015515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06424.404193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14415814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
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_it0.4661.52579
X-RAY DIFFRACTIONr_mcbond_other0.1361.51046
X-RAY DIFFRACTIONr_mcangle_it0.85524182
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47931696
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3524.51584
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1307 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.680.5
2Bmedium positional0.60.5
3Cmedium positional0.750.5
4Dmedium positional0.750.5
1Amedium thermal0.772
2Bmedium thermal0.732
3Cmedium thermal0.722
4Dmedium thermal0.672
LS refinement shellResolution: 2.298→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 127 -
Rwork0.227 2103 -
obs--98.54 %
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)
116.3343-0.76721.64715.61985.466612.74280.00390.255-0.13910.0427-0.19880.3063-0.1807-0.63830.19490.53710.05030.03120.27320.05340.24715.87535.55712.195
23.7038-0.65350.67132.89420.0266.4061-0.10540.20680.03780.43860.11670.2941-0.2148-0.7784-0.01140.28110.036-0.03870.36880.05410.08931.9236.616-1.15
313.7804-2.80540.25864.2153.18375.31-0.0907-0.57960.7917-0.06950.0857-0.0709-0.6532-0.28070.0050.79520.14570.02220.30870.11430.17544.53945.2584.103
45.9255-2.1028-2.28632.0284.18429.7655-0.1611-0.15990.104-0.22490.3765-0.1178-0.73570.8049-0.21540.50180.0193-0.15440.3089-0.00540.14815.04736.5235.277
54.4978-2.03162.91396.8874-4.794511.56670.02310.4854-0.0071-0.0016-0.1248-0.2984-0.07040.17720.10170.31130.0282-0.02250.3029-0.01320.118611.22434.188-4.472
69.31034.76822.520916.616-7.06767.9579-0.13630.3911-0.2252-0.27830.0325-0.42440.56950.08490.10370.42950.0084-0.03430.23510.00350.1718.15225.3555.414
71.78630.3824-0.82244.3832-0.89841.743-0.22410.27150.0184-0.4476-0.02070.3247-0.0414-0.26390.24490.5966-0.0499-0.05750.34630.10740.2216-1.321.53418.113
84.89752.4171-3.08179.4722-0.7312.04470.28970.22970.8103-0.21480.14740.942-0.2496-0.2286-0.43710.70010.0529-0.05750.36490.10760.3303-3.26927.95421.526
93.0034-1.7369-3.07610.85271.15575.7785-0.17370.4735-0.0761-0.84250.1037-0.19260.3699-0.2820.070.6304-0.03060.03410.14750.05040.156.25715.69419.665
102.9789-4.45793.486814.4925-0.68346.83450.07250.1443-0.1878-0.643-0.06810.66980.02430.0992-0.00440.7684-0.1227-0.12890.39580.02770.2367-3.47716.82811.107
116.6403-2.80330.573514.80385.136611.51170.14470.64630.3258-0.3355-0.22710.4212-0.3965-0.51030.08240.60730.00810.05290.10060.04240.19787.34337.28235.306
122.64732.44634.8117.58415.04648.81460.1649-0.20730.1549-0.0584-0.3517-0.79610.24-0.37770.18680.6636-0.05780.110.12940.08510.236710.32237.69144.418
131.8052.4624-3.63827.6297-7.458610.26530.2812-0.71670.05040.4009-0.4568-0.6135-0.29530.82110.17570.7036-0.22140.12430.4919-0.00490.254213.48442.43352.756
144.42660.399-0.32764.9688-1.71695.04060.0903-0.27640.306-0.0528-0.1361-0.443-0.26230.28770.04580.6729-0.02560.17990.03470.00250.210914.00146.98541.478
1510.99940.48684.52274.40770.69867.88050.2017-0.79480.70510.3034-0.0690.3629-1.0011-0.4115-0.13270.7288-0.00310.20350.0701-0.04740.25623.50747.07847.256
161.41330.3694-0.85519.9255.2265.91510.2189-0.18820.04360.1608-0.12880.330.0724-0.3564-0.09010.6227-0.01440.10060.10540.03710.16721.74234.89145.497
171.26920.3618-0.62229.67021.4075.8998-0.03120.0035-0.10670.21230.0308-0.2824-0.03150.2340.00040.5113-0.0012-0.00410.0370.03690.09737.58418.432.714
184.7641-6.58830.93529.66160.81738.6703-0.0757-0.21440.57270.12560.4413-0.995-0.27240.6919-0.36560.6031-0.0943-0.07490.13780.08810.488814.71421.94731.317
194.62214.60910.16549.9488-0.45513.29-0.15170.2330.51220.16150.22780.6556-0.2184-0.3915-0.07610.55030.03910.07040.06310.04470.1957-0.48624.5132.107
208.80915.7714.46827.91650.78835.29610.0728-0.91580.17141.0313-0.12420.24960.0695-0.47360.05140.94370.0485-0.00350.2074-0.00080.17345.01817.69742.595
214.4919-0.40931.084711.47772.629913.78760.0085-0.53430.33150.0271-0.02930.4261-0.4408-0.62870.02080.82150.04320.11360.09080.00940.28527.6758.85833.948
226.12171.4334-6.41421.62351.081112.44190.18670.07440.2836-0.34570.0095-0.053-0.88230.3121-0.19620.93150.0590.13570.30470.21820.398114.43157.82221.737
235.1033-0.40083.35823.53830.823110.51230.13640.48620.2005-0.1466-0.0373-0.409-0.6561.2485-0.09910.7762-0.01080.12640.1710.070.333419.97651.04325.542
2412.7157-2.8801-0.76944.99260.52970.43050.25840.0261-0.3417-0.2826-0.1730.0646-0.01070.0146-0.08540.73080.02230.07980.03090.02830.202510.36746.26829.824
252.9585-1.1346-2.40441.32323.64610.41040.31630.3814-0.3006-0.1165-0.07490.0048-0.1052-0.107-0.24130.81140.06830.03780.16990.01180.37245.50548.78722.29
260.9146-2.1569-0.35310.22544.38056.26670.18250.52310.0574-0.2322-0.230.2227-0.425-0.03830.04750.93730.18290.10060.58090.08660.20625.93557.46321.039
271.772-0.9083-1.36546.6870.86886.26580.0511-0.0434-0.00260.0474-0.1852-0.5450.35660.21930.13410.61320.040.06760.01720.03620.17437.13975.17537.089
283.38885.0641-2.130115.3797.813216.81930.1676-0.1979-0.46230.71420.0165-1.02670.57080.5671-0.18410.69670.0691-0.09040.08530.02350.385511.72172.58743.034
293.6192-1.1609-1.03118.6717-0.81563.64310.02750.0427-0.55740.2227-0.00640.32490.32770.0324-0.02110.7488-0.04860.01890.0296-0.0050.1693-0.13468.86936.438
3010.1442-1.6668-2.5345.1651.08353.01090.10370.7163-0.0522-0.4039-0.0239-0.32890.0119-0.2132-0.07980.65330.00740.07960.06720.03730.18194.85578.12829.341
314.47674.50083.315913.1297-4.705810.5975-0.15390.4912-0.2027-0.14930.0852-0.2072-0.38510.34540.06871.04840.11240.18320.437-0.02060.3679-3.60857.5757.224
322.8838-0.2238-1.063710.27074.71122.49890.495-0.55690.1084-0.1779-0.80160.843-0.2561-0.26080.30651.33320.12350.37540.60110.14770.4633-10.73553.76368.155
331.06280.55713.0679.51362.24089.647-0.02040.09680.07270.24990.26410.2794-0.63530.1465-0.24370.90410.03250.21990.20640.12520.3626-3.85147.68661.055
340.38050.98241.55322.5734.0456.42510.0020.1048-0.11640.14710.3252-0.33850.07840.6384-0.32721.5817-0.1403-0.05920.70470.41310.73121.59753.62169.823
350.2933-1.69951.116212.106-5.73054.7733-0.2085-0.099-0.05480.88360.32820.1735-0.5773-0.2455-0.11971.2236-0.02320.23980.42750.05370.2683-3.02161.29467.801
368.0628-2.9874-4.336119.216-6.805813.07390.1343-0.56090.30911.5042-0.1535-0.80670.13120.4650.01931.0947-0.03520.08160.13810.03080.1776-2.93269.86955.599
372.0773-0.07471.12216.5498-1.6889.70620.0704-0.0359-0.04080.2625-0.03480.74150.3409-0.4346-0.03560.5801-0.03360.14990.08680.03250.202-10.31271.55344.075
387.84735.2751-1.66237.9915-4.54423.02010.29750.4618-0.74580.53430.0020.1342-0.16120.15-0.29941.08380.00550.11540.1411-0.02510.2798-0.4865.9147.803
3912.10441.348-2.263710.59180.78092.6804-0.0365-0.49971.00040.9946-0.02430.0722-0.14010.08290.06080.8499-0.0240.02220.1161-0.00130.2040.67279.49749.91
409.31642.0913-3.16349.945.11559.541-0.2544-0.940.35630.88420.0548-0.1039-0.17390.11660.19960.89430.07190.22060.1859-0.05780.3165-11.20676.6255.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 14
2X-RAY DIFFRACTION2A15 - 37
3X-RAY DIFFRACTION3A38 - 52
4X-RAY DIFFRACTION4A53 - 59
5X-RAY DIFFRACTION5A60 - 72
6X-RAY DIFFRACTION6A73 - 78
7X-RAY DIFFRACTION7A79 - 94
8X-RAY DIFFRACTION8A95 - 113
9X-RAY DIFFRACTION9A114 - 125
10X-RAY DIFFRACTION10A126 - 138
11X-RAY DIFFRACTION11B9 - 14
12X-RAY DIFFRACTION12B15 - 22
13X-RAY DIFFRACTION13B23 - 35
14X-RAY DIFFRACTION14B36 - 54
15X-RAY DIFFRACTION15B55 - 67
16X-RAY DIFFRACTION16B68 - 81
17X-RAY DIFFRACTION17B82 - 97
18X-RAY DIFFRACTION18B98 - 106
19X-RAY DIFFRACTION19B107 - 124
20X-RAY DIFFRACTION20B125 - 138
21X-RAY DIFFRACTION21C8 - 16
22X-RAY DIFFRACTION22C17 - 28
23X-RAY DIFFRACTION23C29 - 43
24X-RAY DIFFRACTION24C44 - 55
25X-RAY DIFFRACTION25C56 - 64
26X-RAY DIFFRACTION26C65 - 78
27X-RAY DIFFRACTION27C79 - 99
28X-RAY DIFFRACTION28C100 - 105
29X-RAY DIFFRACTION29C106 - 121
30X-RAY DIFFRACTION30C122 - 138
31X-RAY DIFFRACTION31D10 - 20
32X-RAY DIFFRACTION32D21 - 34
33X-RAY DIFFRACTION33D35 - 55
34X-RAY DIFFRACTION34D56 - 64
35X-RAY DIFFRACTION35D65 - 78
36X-RAY DIFFRACTION36D79 - 83
37X-RAY DIFFRACTION37D84 - 104
38X-RAY DIFFRACTION38D105 - 114
39X-RAY DIFFRACTION39D115 - 125
40X-RAY DIFFRACTION40D126 - 138

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