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- PDB-3mdy: Crystal structure of the cytoplasmic domain of the bone morphogen... -

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Basic information

Entry
Database: PDB / ID: 3mdy
TitleCrystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189
Components
  • Bone morphogenetic protein receptor type-1B
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsTransferase/isomerase / COMPLEX (ISOMERASE-PROTEIN KINASE) / RECEPTOR SERINE/THREONINE KINASE / Structural Genomics Consortium / SGC / ATP-binding / Disease mutation / Kinase / Transferase / Rotamase / Transferase-isomerase complex
Function / homology
Function and homology information


negative regulation of chondrocyte proliferation / ovulation cycle / ovarian cumulus expansion / chondrocyte development / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / BMP binding / proteoglycan biosynthetic process / endochondral bone morphogenesis / positive regulation of cartilage development / positive regulation of chondrocyte differentiation ...negative regulation of chondrocyte proliferation / ovulation cycle / ovarian cumulus expansion / chondrocyte development / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / BMP binding / proteoglycan biosynthetic process / endochondral bone morphogenesis / positive regulation of cartilage development / positive regulation of chondrocyte differentiation / BMP receptor activity / macrolide binding / activin receptor binding / transforming growth factor beta receptor activity, type I / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / eye development / cytoplasmic side of membrane / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / cellular response to BMP stimulus / TGFBR1 LBD Mutants in Cancer / Signaling by BMP / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / dorsal/ventral pattern formation / retinal ganglion cell axon guidance / regulation of amyloid precursor protein catabolic process / terminal cisterna / signaling receptor inhibitor activity / ryanodine receptor complex / central nervous system neuron differentiation / 'de novo' protein folding / cartilage condensation / ventricular cardiac muscle tissue morphogenesis / FK506 binding / SMAD binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / HFE-transferrin receptor complex / cellular response to growth factor stimulus / Z disc / SARS-CoV-1 activates/modulates innate immune responses / osteoblast differentiation / transmembrane signaling receptor activity / protein folding / regulation of protein localization / retina development in camera-type eye / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / receptor complex / inflammatory response / neuronal cell body / protein serine/threonine kinase activity / dendrite / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Chitinase A; domain 3 - #40 / Snake toxin-like superfamily / : ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Chitinase A; domain 3 - #40 / Snake toxin-like superfamily / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LDN / Bone morphogenetic protein receptor type-1B / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChaikuad, A. / Sanvitale, C. / Mahajan, P. / Daga, N. / Cooper, C. / Krojer, T. / Alfano, I. / Knapp, S. / von Delft, F. / Weigelt, J. ...Chaikuad, A. / Sanvitale, C. / Mahajan, P. / Daga, N. / Cooper, C. / Krojer, T. / Alfano, I. / Knapp, S. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189
Authors: Chaikuad, A. / Sanvitale, C. / Mahajan, P. / Daga, N. / Cooper, C. / Krojer, T. / Alfano, I. / Knapp, S. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / ...Authors: Chaikuad, A. / Sanvitale, C. / Mahajan, P. / Daga, N. / Cooper, C. / Krojer, T. / Alfano, I. / Knapp, S. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / 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_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 / _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: Bone morphogenetic protein receptor type-1B
C: Bone morphogenetic protein receptor type-1B
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
D: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5536
Polymers100,7404
Non-polymers8132
Water12,376687
1
A: Bone morphogenetic protein receptor type-1B
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7763
Polymers50,3702
Non-polymers4061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area19120 Å2
MethodPISA
2
C: Bone morphogenetic protein receptor type-1B
D: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7763
Polymers50,3702
Non-polymers4061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.410, 80.010, 183.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21B
12A
22C
13C
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLUGLU2DD0 - 1081 - 109
211SERSERGLUGLU2BC0 - 1081 - 109
112GLUGLUSERSER4AA174 - 1759 - 10
212GLUGLUSERSER4CB174 - 1759 - 10
122ARGARGASPASP4AA177 - 17812 - 13
222ARGARGASPASP4CB177 - 17812 - 13
132ILEILEGLYGLY4AA180 - 18915 - 24
232ILEILEGLYGLY4CB180 - 18915 - 24
142SERSERILEILE2AA190 - 20425 - 39
242SERSERILEILE2CB190 - 20425 - 39
152METMETLYSLYS2AA206 - 22241 - 57
252METMETLYSLYS2CB206 - 22241 - 57
113GLUGLUMETMET2CB226 - 25361 - 88
213GLUGLUMETMET2AA226 - 25361 - 88
123HISHISGLYGLY2CB255 - 26890 - 103
223HISHISGLYGLY2AA255 - 26890 - 103
133THRTHRTHRTHR6CB269 - 273104 - 108
233THRTHRTHRTHR6AA269 - 273104 - 108
143GLNGLNLYSLYS2CB274 - 356109 - 191
243GLNGLNLYSLYS2AA274 - 356109 - 191
153THRTHRASNASN4CB370 - 388205 - 223
253THRTHRASNASN4AA370 - 388205 - 223
163ASNASNILEILE2CB390 - 500225 - 335
263ASNASNILEILE2AA390 - 500225 - 335

NCS ensembles :
ID
1
2
3
DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Bone morphogenetic protein receptor type-1B / BMPR1B / BMP type-1B receptor / BMPR-1B


Mass: 38315.078 Da / Num. of mol.: 2
Fragment: BMPR1B cytoplasmic (GS and kinase) domain (residue 168-502)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1B / Plasmid: pFB-LIC-Bse / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O00238, receptor protein serine/threonine kinase
#2: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / FKBP12 / PPIase FKBP1A / FK506-binding protein 1A / FKBP-1A / Rotamase / Immunophilin FKBP12 / 12 ...FKBP12 / PPIase FKBP1A / FK506-binding protein 1A / FKBP-1A / Rotamase / Immunophilin FKBP12 / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12


Mass: 12054.782 Da / Num. of mol.: 2 / Fragment: FKBP12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP12 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P62942, peptidylprolyl isomerase
#3: Chemical ChemComp-LDN / 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline


Mass: 406.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.2M Na Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2010 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→48.79 Å / Num. all: 61055 / Num. obs: 60968 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8618 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 3H9R CHAIN A, and CHAIN B

3h9r


Resolution: 2.05→44.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.793 / SU B: 9.983 / SU ML: 0.142 / SU R Cruickshank DPI: 0.219 / SU Rfree: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 3085 5.1 %RANDOM
Rwork0.20145 57883 --
obs0.2042 57883 99.54 %-
all-60968 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.3 Å2 / Biso mean: 26.029 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--2.56 Å20 Å2
3----1.83 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.05→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 62 687 7476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227003
X-RAY DIFFRACTIONr_bond_other_d0.0020.024873
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9739471
X-RAY DIFFRACTIONr_angle_other_deg0.9263.00111820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44923.379290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.462151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7071547
X-RAY DIFFRACTIONr_chiral_restr0.0910.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217697
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021406
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_it3.70634283
X-RAY DIFFRACTIONr_mcbond_other0.89431753
X-RAY DIFFRACTIONr_mcangle_it5.48656906
X-RAY DIFFRACTIONr_scbond_it7.43482720
X-RAY DIFFRACTIONr_scangle_it9.839112555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11D633tight positional0.020.05
21A186tight positional0.040.05
31C1396tight positional0.040.05
12B796medium positional0.060.5
22C396medium positional0.040.5
32A1987medium positional0.050.5
31C61loose positional0.085
11D633tight thermal0.150.5
21A186tight thermal0.180.5
31C1396tight thermal0.210.5
12B796medium thermal0.112
22C396medium thermal0.12
32A1987medium thermal0.162
31C61loose thermal0.210
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 234 -
Rwork0.301 4071 -
all-4305 -
obs--96.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.03982.4462-0.23782.0275-1.00774.96020.195-0.83120.4860.1428-0.13030.2994-0.1144-0.4082-0.06470.0414-0.01010.02360.2287-0.06910.057924.96756.759355.9651
20.76160.02090.95590.12170.23451.5606-0.05270.14720.03370.029-0.07610.0435-0.01230.05760.12870.08390.00210.01720.12120.02430.088338.14294.840151.1508
30.59610.01110.46160.06180.14070.6427-0.05040.00280.0480.0244-0.01820.01740.0232-0.02590.06860.09820.00230.01040.06060.01690.092344.16382.728565.0923
40.82810.52250.61530.57650.03341.0699-0.01290.00220.01950.0083-0.0693-0.00810.07250.15950.08220.09290.05050.02480.09390.04760.07958.1916-2.409870.3249
52.7838-0.3681-1.80420.7101-0.23261.64750.09260.32460.1331-0.03610.0723-0.085-0.0667-0.4259-0.16490.0124-0.00440.01990.25370.08780.101712.67524.012444.9094
61.7971-0.6463-1.38881.3802-0.35011.7025-0.14410.1657-0.0282-0.00650.1490.02870.1451-0.2937-0.00490.0143-0.0346-0.00320.2212-0.00290.026916.2287-1.25744.3658
74.9327-1.34111.66871.5684-0.33333.3397-0.02620.80250.3704-0.1715-0.1098-0.28-0.10970.7010.1360.0754-0.01640.02720.3070.06280.085340.64696.688813.0983
80.4684-0.18850.22680.620.02470.62310.0379-0.0790.020.0141-0.029-0.1144-0.02090.0749-0.0090.0778-0.01580.020.05610.00040.072827.04055.1517.8387
90.68790.09160.25440.02440.08240.9394-0.0202-0.01210.0145-0.0186-0.0261-0.00240.01540.05690.04630.09020.01140.01290.07960.00710.083622.30682.24887.5905
100.5792-0.22910.70610.9163-0.10121.41190.01260.02140.012-0.0964-0.11030.0180.1366-0.32560.09770.0742-0.06290.02730.2325-0.05410.06097.0158-2.0467-0.9074
114.70330.15-1.24690.40190.53291.17360.0058-0.45950.18220.04590.1313-0.03230.07690.4194-0.13710.04680.0417-0.00060.3961-0.08440.041255.06322.255723.6425
125.13470.3814-1.96460.83760.3431.66950.0126-0.31850.1608-0.00520.17430.11180.02260.5095-0.18680.02950.0212-0.00160.2306-0.05180.073749.71962.271225.8548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A174 - 202
2X-RAY DIFFRACTION2A203 - 273
3X-RAY DIFFRACTION3A274 - 369
4X-RAY DIFFRACTION4A370 - 502
5X-RAY DIFFRACTION5B0 - 67
6X-RAY DIFFRACTION6B68 - 108
7X-RAY DIFFRACTION7C174 - 201
8X-RAY DIFFRACTION8C202 - 256
9X-RAY DIFFRACTION9C257 - 373
10X-RAY DIFFRACTION10C374 - 500
11X-RAY DIFFRACTION11D0 - 43
12X-RAY DIFFRACTION12D44 - 108

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