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- PDB-3rez: glycoprotein GPIb variant -

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Basic information

Entry
Database: PDB / ID: 3rez
Titleglycoprotein GPIb variant
ComponentsPlatelet glycoprotein Ib beta chain, Platelet glycoprotein IX
KeywordsCELL ADHESION / platelet surface receptor / Glycoprotein / GP1BB and GPIX
Function / homology
Function and homology information


glycoprotein Ib-IX-V complex / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / plasma membrane => GO:0005886 / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol ...glycoprotein Ib-IX-V complex / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / plasma membrane => GO:0005886 / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol / Intrinsic Pathway of Fibrin Clot Formation / platelet activation / transmembrane signaling receptor activity / blood coagulation / cell surface receptor signaling pathway / cell adhesion / identical protein binding / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...Leucine rich repeat C-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
beta-L-fucopyranose / alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER / Platelet glycoprotein Ib beta chain / Platelet glycoprotein IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMcEwan, P.A. / Yang, W. / Carr, K.H. / Mo, X. / Zheng, X. / Li, R. / Emsley, J.
CitationJournal: Blood / Year: 2011
Title: Quaternary organization of GPIb-IX complex and insights into Bernard-Soulier syndrome revealed by the structures of GPIb beta and a GPIb beta/GPIX chimera
Authors: McEwan, P.A. / Yang, W. / Carr, K.H. / Mo, X. / Zheng, X. / Li, R. / Emsley, J.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
B: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
C: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
D: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,54218
Polymers56,3494
Non-polymers2,19314
Water4,918273
1
A: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4143
Polymers14,0871
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4143
Polymers14,0871
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0867
Polymers14,0871
Non-polymers9996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6275
Polymers14,0871
Non-polymers5404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.010, 72.010, 171.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A10 - 100
2114B10 - 100
3114C10 - 100
4114D10 - 100

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX / GP-Ib beta / GPIb-beta / GPIbB / Antigen CD42b-beta / GP-IX / GPIX / Glycoprotein 9


Mass: 14087.135 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GP1BB and GPIX chimeria / Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BB, GP9 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P13224, UniProt: P14770

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Sugars , 3 types, 7 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-FUL / beta-L-fucopyranose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 280 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M MMT buffer pH 5 (MMT buffer is a mixture of DL-malic acid, MES and Tris base in the molar ratios 1:2:2 DL-malic acid:MES:Tris base), 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å
DetectorType: MARC MOSAIC3 / Detector: CCD / Date: Jun 18, 2010
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→62.36 Å / Num. obs: 23135 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→42.17 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.891 / SU B: 16.842 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.51 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25925 1036 5 %RANDOM
Rwork0.21146 ---
obs0.2139 19566 92.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 118 273 3864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223722
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3012.0345105
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85520.548146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1115526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3861552
X-RAY DIFFRACTIONr_chiral_restr0.0730.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222832
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.1781.52311
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.3523724
X-RAY DIFFRACTIONr_scbond_it0.83631411
X-RAY DIFFRACTIONr_scangle_it1.4874.51376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 692 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.250.5
Bmedium positional0.340.5
Cmedium positional0.270.5
Dmedium positional0.290.5
Amedium thermal0.312
Bmedium thermal0.342
Cmedium thermal0.282
Dmedium thermal0.332
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 92 -
Rwork0.235 1559 -
obs--100 %
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)
14.1977-2.59834.91231.6104-3.014111.565-0.16530.33970.37530.0694-0.2324-0.2301-0.9641-0.3420.39770.3480.1226-0.01770.28130.01610.307434.4329-0.76580.0693
210.81192.79226.35110.94122.69999.7792-0.0312-0.35840.1638-0.0074-0.20790.1814-0.0548-0.64880.23910.10560.0440.05070.146-0.080.390335.3357-7.82730.2475
314.13728.92280.90166.31120.79150.13090.3409-0.44880.1107-0.0601-0.35470.0607-0.0593-0.05220.01390.28910.0586-0.00430.2010.01980.230836.3507-3.3741-7.0228
43.34712.6152-0.54343.48750.85572.3080.07150.2310.3482-0.0297-0.08680.46360.0766-0.27930.01530.14430.10230.00540.12840.00240.081236.7371-10.108-9.7605
53.93180.9912-0.41693.1926-0.321.90280.05890.23160.0126-0.20390.0066-0.001-0.1501-0.0988-0.06550.10460.02450.00170.0732-0.01450.059544.1038-12.6005-12.0129
61.1366-0.1525-1.65934.2316-2.01883.76350.01470.0689-0.23660.162-0.2468-0.0781-0.1138-0.06790.23210.1405-0.002-0.01490.12210.05110.260743.1637-20.9593-8.4553
78.0882-2.87673.70834.1313-2.302711.4294-0.34460.5219-0.1916-0.5365-0.0270.1485-0.2371-0.22480.37160.212-0.0078-0.06710.1127-0.080.132938.7664-25.3267-19.8236
820.9078-8.572611.101825.4528-3.11825.99720.96851.62420.9577-0.9614-1.3711-1.82170.4010.85820.40260.79-0.06440.10090.7259-0.08590.515942.3445-22.3035-27.2351
915.92020.135718.13950.02080.09320.8756-0.21260.13080.5250.0822-0.04330.0873-0.44820.24230.25590.502-0.17080.12330.2237-0.07230.726345.8434-16.5123-49.2705
107.635-1.66111.95180.4897-1.27578.2967-0.05880.24670.05420.1369-0.0865-0.1019-0.28320.19360.14530.3125-0.0913-0.14140.12910.01890.251745.0457-23.8274-50.2123
114.4713-1.36240.82594.0358-0.96620.31410.1770.3250.55490.0367-0.2278-0.0353-0.05090.13140.05080.3156-0.06320.00240.1979-0.0930.200841.9324-19.9364-43.5277
124.0433-1.38820.02483.1951-0.21923.2930.10630.00330.1868-0.0063-0.0573-0.0084-0.19920.028-0.0490.0786-0.0284-0.01190.0552-0.04560.081538.24-27.1171-43.2003
1314.9148-7.17499.52493.4645-4.586.0848-0.6031-1.03310.41140.26360.3921-0.1564-0.3651-0.67550.2110.25330.0008-0.02360.4153-0.14360.264536.032-34.0301-30.7039
147.1075-2.933-1.00255.49161.80322.50190.09060.2309-0.173-0.1406-0.17360.00880.0319-0.22570.0830.0902-0.0084-0.00930.0336-0.0240.029130.6782-34.4287-44.7029
154.13091.69374.51575.3721.51464.9960.193-0.4167-0.05710.335-0.1620.10460.1639-0.381-0.03090.1343-0.0371-0.04180.21490.05490.060638.5164-42.7523-34.2404
160.3905-1.72860.12137.6615-0.54260.0433-0.07990.01760.50690.3165-0.0595-2.2349-0.0348-0.05060.13940.5295-0.05970.06270.6663-0.07580.705833.5984-40.3349-26.4534
170.06430.0822-0.16720.6633-2.22917.88130.0714-0.08330.0878-0.02030.23430.21110.1681-0.9825-0.30570.1597-0.12960.03420.3064-0.05440.569436.3953-44.9749-1.5459
185.7895-1.0603-0.05684.10524.44119.30060.07560.1119-0.34380.05530.25290.3570.4811-0.0408-0.32850.1831-0.1267-0.00580.1220.01380.270441.3433-48.4819-9.9543
1924.85961.88834.7219.5388-1.187711.7124-0.016-0.2107-0.08830.3544-0.25260.5197-0.15-0.81860.26860.1716-0.03040.0240.13940.00620.124736.2184-36.2798-3.8844
202.9035-2.88911.01233.097-1.21390.5463-0.01840.1068-0.3341-0.1680.03430.23320.1614-0.0951-0.01590.1828-0.12150.04110.125-0.05950.160244.4343-42.3362-13.7386
213.0658-1.341-1.21232.5132-0.06264.98960.04160.09030.0020.0395-0.06970.1875-0.08-0.28580.02820.0772-0.0432-0.00850.0611-0.03720.124946.8254-37.3952-14.4652
225.87180.81992.83569.4178-2.29152.147-0.04430.00820.36480.6665-0.1833-0.1179-0.20630.06080.22760.1299-0.02380.02860.0819-0.02130.05452.571-31.9898-9.6087
232.60691.01121.32382.46932.9883.70370.0930.0854-0.4461-0.1859-0.14730.0269-0.0806-0.06320.05430.28430.1360.05970.20510.00390.13458.7605-41.8983-21.5348
2411.69170.227414.03535.39282.242417.6937-0.38860.41790.2259-0.34690.2663-0.2358-0.79440.51630.12230.3776-0.00320.06760.34820.02690.172154.2406-33.8683-30.0379
253.27081.64462.4077.5449-3.20194.6867-0.41780.28120.1693-0.1702-0.0494-0.5154-0.33670.37530.46720.2287-0.07190.06110.1642-0.08940.186577.0956-0.1716-4.1358
264.1961-1.57412.59562.0264-1.97512.3157-0.03450.13170.18470.0629-0.0945-0.1836-0.06070.10360.1290.2567-0.10490.09480.1698-0.03870.269776.79-2.1148-11.5823
274.1693-1.2480.4732.74180.5433.0982-0.04260.11260.0962-0.06660.0837-0.1360.03810.1288-0.04110.0841-0.06440.04060.0727-0.03170.02670.3244-6.3814-11.1707
2811.47463.078510.14079.96564.67689.3869-0.11870.70550.4554-1.1982-0.1538-0.6513-0.39180.51150.27250.35360.04130.11480.24420.02010.094662.0413-2.778-21.8763
294.4668-0.1769-7.371614.3994-5.400214.47280.10870.0351-0.2171-0.0133-0.28690.1516-0.1930.00890.17830.0098-0.0076-0.00140.04750.07320.243463.8768-14.4133-13.0551
302.2295-0.60812.16933.1393-2.52613.3883-0.1226-0.01920.1598-0.070.03590.0392-0.1174-0.06110.08670.22730.05090.05670.1481-0.00540.038756.6619-3.9306-14.8467
316.8243-0.06170.14988.2348-4.0127.5167-0.27720.33090.1873-0.41780.0061-0.01070.1356-0.41380.2710.130.00830.00690.1387-0.05630.047552.5455-5.9733-17.7227
321.1802-1.4567-4.07271.80035.032214.0706-0.4740.2148-0.30120.4126-0.37250.35521.2037-0.70660.84650.75180.02160.00810.67710.05110.819655.074-10.7527-26.7105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 8
2X-RAY DIFFRACTION2A9 - 16
3X-RAY DIFFRACTION3A17 - 28
4X-RAY DIFFRACTION4A29 - 44
5X-RAY DIFFRACTION5A45 - 79
6X-RAY DIFFRACTION6A80 - 91
7X-RAY DIFFRACTION7A92 - 106
8X-RAY DIFFRACTION8A107 - 113
9X-RAY DIFFRACTION9B0 - 8
10X-RAY DIFFRACTION10B9 - 16
11X-RAY DIFFRACTION11B17 - 28
12X-RAY DIFFRACTION12B29 - 63
13X-RAY DIFFRACTION13B64 - 70
14X-RAY DIFFRACTION14B71 - 87
15X-RAY DIFFRACTION15B88 - 107
16X-RAY DIFFRACTION16B108 - 113
17X-RAY DIFFRACTION17C-1 - 11
18X-RAY DIFFRACTION18C12 - 24
19X-RAY DIFFRACTION19C25 - 30
20X-RAY DIFFRACTION20C31 - 47
21X-RAY DIFFRACTION21C48 - 73
22X-RAY DIFFRACTION22C74 - 87
23X-RAY DIFFRACTION23C88 - 104
24X-RAY DIFFRACTION24C105 - 115
25X-RAY DIFFRACTION25D0 - 16
26X-RAY DIFFRACTION26D17 - 28
27X-RAY DIFFRACTION27D29 - 61
28X-RAY DIFFRACTION28D62 - 69
29X-RAY DIFFRACTION29D70 - 82
30X-RAY DIFFRACTION30D83 - 96
31X-RAY DIFFRACTION31D97 - 105
32X-RAY DIFFRACTION32D106 - 110

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