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- PDB-4egx: Crystal structure of KIF1A CC1-FHA tandem -

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Basic information

Entry
Database: PDB / ID: 4egx
TitleCrystal structure of KIF1A CC1-FHA tandem
ComponentsKinesin-like protein KIF1A
KeywordsTRANSPORT PROTEIN / FHA domain
Function / homology
Function and homology information


neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Kinesins / plus-end-directed microtubule motor activity ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / neuronal dense core vesicle / cytoskeletal motor activity / axon cytoplasm / vesicle-mediated transport / microtubule binding / microtubule / axon / dendrite / synapse / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2520 / : / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Tumour Suppressor Smad4 - #20 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2520 / : / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Helix non-globular / Special / PH-like domain superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Kinesin-like protein KIF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsYu, J. / Huo, L. / Yue, Y. / Xu, T. / Zhang, M. / Feng, W.
CitationJournal: Structure / Year: 2012
Title: The CC1-FHA Tandem as a Central Hub for Controlling the Dimerization and Activation of Kinesin-3 KIF1A
Authors: Huo, L. / Yue, Y. / Ren, J. / Yu, J. / Liu, J. / Yu, Y. / Ye, F. / Xu, T. / Zhang, M. / Feng, W.
History
DepositionApr 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF1A
B: Kinesin-like protein KIF1A
C: Kinesin-like protein KIF1A
D: Kinesin-like protein KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2558
Polymers83,8594
Non-polymers3964
Water2,882160
1
A: Kinesin-like protein KIF1A
B: Kinesin-like protein KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1284
Polymers41,9292
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-31 kcal/mol
Surface area20020 Å2
MethodPISA
2
C: Kinesin-like protein KIF1A
D: Kinesin-like protein KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1284
Polymers41,9292
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-32 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.943, 87.855, 101.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Kinesin-like protein KIF1A / Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A- ...Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A-related protein / hUnc-104


Mass: 20964.643 Da / Num. of mol.: 4 / Fragment: CC1-FHA tandem, UNP residues 430-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF1A, ATSV, C2orf20 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q12756
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 18% (w/v) PEG 5000 MME, 8% (v/v) Tacsimate (pH 6.0), 0.1 M Bis-Tris, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 25983 / Num. obs: 24084 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.8
Reflection shellResolution: 2.5→2.54 Å / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FM8
Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.86 / SU B: 24.207 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 1.174 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28257 1286 5.1 %RANDOM
Rwork0.25168 ---
obs0.25325 24084 96.36 %-
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: 39.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--1.89 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5405 0 26 160 5591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.977416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71323.574249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.81715960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6431550
X-RAY DIFFRACTIONr_chiral_restr0.0780.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.22292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23615
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.2167
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5371.53579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6725583
X-RAY DIFFRACTIONr_scbond_it1.07632118
X-RAY DIFFRACTIONr_scangle_it1.6334.51833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.511→2.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 89 -
Rwork0.305 1500 -
obs--83.11 %
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)
11.89251.0224-0.1562.98371.10549.7630.25820.298-0.2037-0.5097-0.2431-0.22260.69880.1337-0.015-0.01690.04620.05610.0933-0.02970.0541-7.823-17.7202-70.0754
27.21923.90494.47932.11222.42292.77920.1739-0.36330.1430.1473-0.1102-0.17390.22780.0691-0.06370.0694-0.03230.02990.21810.00040.15024.5293-5.8821-47.0574
34.08570.6119-2.24751.89033.017915.71470.1766-0.2891-0.30450.0359-0.08280.44220.37510.5308-0.0938-0.03830.0007-0.01310.1207-0.10750.117512.15632.7846-26.8255
48.12852.79224.00873.18450.27083.376-0.54920.1336-0.5235-0.57470.17080.4151-0.0101-0.42020.37850.10.0151-0.03390.1527-0.06110.117911.78952.0333-18.1848
51.32670.7366-0.98560.4089-0.53873.9840.0881-0.21420.1593-0.1806-0.03560.1158-0.0961-0.1892-0.05250.0128-0.0047-0.03040.0602-0.01820.098916.864515.7663-11.8173
67.1928-3.6083-4.83122.38661.27283.3090.25221.06110.7524-0.316-0.8825-0.4278-1.29440.21860.63030.2088-0.0085-0.09710.12290.00960.085724.924528.6197-14.9749
72.7621-0.9984-0.17231.75150.17411.39990.15430.2618-0.0643-0.1293-0.041-0.0810.08820.3336-0.11330.04220.0040.01270.1203-0.00820.032327.165120.1073-11.1386
82.1121-2.1473-0.13092.6145-0.61891.3187-0.056-0.28020.02970.17430.08-0.3088-0.12580.2298-0.02390.0161-0.0420.00820.1069-0.01350.050728.808517.518-0.3992
94.5689-7.0378-1.644812.07792.49050.5937-0.0261-0.0572-0.08070.1034-0.04250.36310.1054-0.23820.06860.0173-0.00450.00730.12310.0420.092819.412115.2787-3.1777
100.63732.0454-0.865947.642-10.43072.60190.219-1.0677-0.50620.20990.4448-0.48080.2962-1.5922-0.66390.15880.0014-0.06560.1260.1041-0.046325.3886-1.5575-4.5729
119.12664.97044.53927.56934.29377.1977-0.10070.3972-0.18070.04050.34420.05580.01570.2569-0.2435-0.03580.0606-0.00050.04590.04360.0787-20.1818-13.8363-61.8476
1210.11076.02356.67458.24877.28326.7526-0.4594-0.52921.02270.7512-0.17670.5924-0.690.00590.63610.2177-0.141-0.01970.04440.04990.0127-4.8193-0.9362-45.6561
131.1841-1.8063-0.4252.75540.64830.15260.04160.77381.49560.4145-0.1231.06660.52730.16820.08140.2022-0.1025-0.11030.1746-0.08180.19188.642710.9335-29.4609
149.70454.0002-4.86852.3984-0.55235.26510.01191.22980.7043-0.10630.12250.06160.1024-0.4444-0.1345-0.01640.0208-0.0520.0574-0.03030.069420.471715.8247-20.4082
153.3502-1.66011.24686.02180.774814.02560.45150.52620.2466-0.4227-0.56250.01060.51790.89040.111-0.0224-0.10290.01140.1293-0.04090.08634.941811.078-11.5538
165.66621.7293-0.35152.8662-1.4880.83710.0939-2.1173-0.87430.33930.08720.00990.6397-0.1462-0.18110.3982-0.0921-0.26760.2219-0.13770.333211.65511.0927-9.032
174.981-0.67230.31133.8224-1.47424.625-0.06250.331-0.4994-0.42790.1488-0.01660.4604-0.1806-0.08630.01250.0137-0.02490.0477-0.10980.0018-2.48-0.2469-16.2369
182.7789-0.79781.12093.9775-0.39323.6086-0.08510.057-0.1902-0.02750.27920.41190.0902-0.4866-0.1941-0.0287-0.0382-0.03380.0885-0.02790.066-8.42264.5311-10.3941
196.86421.786-0.81994.81460.63484.4894-0.1092-0.5498-0.0943-0.3670.12910.24010.33750.0572-0.0199-0.04180.0414-0.00630.0101-0.01710.0875-8.487210.6952-4.7618
204.1215-1.48441.2358.8977-5.23375.3849-0.13410.14790.23140.0290.08180.0667-0.359-0.09040.05230.07240.0155-0.02380.0997-0.03940.0452-0.766913.6162-9.4356
212.0941-2.2551-0.845.3569-1.42585.42570.12890.150.3431-0.4280.0055-0.3704-0.20030.1962-0.1344-0.01350.0479-0.01090.06070.02020.132530.7302-28.5354-49.6175
222.28260.5224-2.46512.7463.95410.43490.67-0.33160.51790.3473-0.22370.0185-1.0956-0.2852-0.44630.16760.0340.03880.0679-0.03630.074320.163-16.9343-24.4096
236.66582.91487.23894.1159-1.819116.60550.79740.6866-0.5482-0.7236-1.1206-0.9158-0.21060.20540.32320.19630.00240.11770.09480.084-0.026516.5859-12.7308-1.6435
242.55131.3364-2.82730.7-1.48093.133-0.16510.16270.03270.54990.1356-0.64221.08440.77680.02950.258-0.01960.01050.1214-0.0009-0.02518.0407-10.95427.0857
250.6263-1.28311.56617.1686-3.84594.00570.2881-0.18760.05960.3120.2590.54580.6127-0.5886-0.54710.047-0.06840.0310.0653-0.08810.07355.018-8.013814.779
262.12683.0770.21224.79731.65175.25340.14160.15290.0273-0.2909-0.0401-0.1418-0.5759-0.0682-0.10150.01460.0041-0.01580.1020.0458-0.01077.58922.62611.1086
277.1977-2.2783-1.69141.8432-2.3757.94670.0935-0.0304-0.28050.0206-0.06560.37630.2749-0.5263-0.02790.01450.08440.0202-0.01080.00250.1052-2.68344.15915.57
2810.09551.9976-5.40044.3472-0.31774.0697-0.1152-0.0664-0.17190.08230.0703-0.3054-0.27710.03910.04490.04050.0617-0.03730.00950.0034-0.00339.34798.885920.2646
292.80880.11970.33193.4201-0.05412.5135-0.1055-0.09070.01040.48620.02390.26270.2314-0.1120.08160.17810.0365-0.00190.1593-0.0099-0.03287.07552.61225.5077
3016.6906-0.25241.95582.95590.68960.563-0.2176-0.7032-0.19880.24960.0799-0.7495-0.10150.13640.13780.07090.012-0.02520.06490.00860.069217.6980.489119.7554
3122.3981-0.6067-9.09128.85526.28067.8098-0.4375-0.2345-1.10080.910.0355-0.29461.53770.75870.402-0.0010.1521-0.12950.14430.13010.104739.2456-40.7847-42.5104
325.368-6.3798-7.39179.47589.360314.4127-0.3855-0.1871-0.23240.67090.03740.11560.6995-0.22030.34810.0175-0.0095-0.05020.10840.08260.082826.2576-30.6989-27.6593
332.534-2.3511-2.42192.18332.20113.3787-0.31230.33890.06070.01950.06910.29460.4327-0.22670.24320.1440.01860.05030.1416-0.06410.07119.4644-13.1078-5.3593
341.12041.41150.38053.9895-0.57150.62860.06990.10020.0047-0.412-0.01980.17630.1201-0.1299-0.05020.14460.03660.03450.0636-0.049-0.01257.8382-12.27139.3367
3519.6586-7.2445-9.98282.66973.67885.06930.6790.63250.22970.5318-0.2812-1.07820.13372.2127-0.39780.219-0.20210.13650.03780.08180.233220.5394-12.114215.8611
361.13370.9676-0.80532.59340.73751.7206-0.08630.6051-0.1528-0.4384-0.01170.02890.39690.51640.0980.21030.10430.01770.0165-0.05380.00414.9569-25.01647.472
3710.0149-3.4794-2.46542.6254-2.157910.16910.6153-0.21720.6397-0.0889-0.1719-0.6496-0.04821.2894-0.4434-0.04060.11320.0443-0.0208-0.04950.115623.7998-26.466214.5903
383.4671-2.32970.16182.11360.56465.61340.51140.2643-0.2438-0.1112-0.33320.51481.37670.1247-0.17810.1442-0.0139-0.1079-0.1325-0.01510.16149.2518-32.433310.6364
397.3753-0.6383-1.2392.6374-0.4015.2642-0.14340.1094-0.15640.1503-0.00190.13230.78250.11430.14530.1613-0.04270.0063-0.0411-0.0061-0.04519.688-29.648721.719
406.9898-2.08381.43424.0480.3420.4671-0.06220.3813-0.4695-0.29960.15230.36680.0922-0.1348-0.09010.0297-0.0977-0.03960.07180.0340.00257.3654-22.06515.8635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A424 - 441
2X-RAY DIFFRACTION2A442 - 463
3X-RAY DIFFRACTION3A464 - 477
4X-RAY DIFFRACTION4A478 - 492
5X-RAY DIFFRACTION5A493 - 516
6X-RAY DIFFRACTION6A517 - 524
7X-RAY DIFFRACTION7A525 - 553
8X-RAY DIFFRACTION8A554 - 581
9X-RAY DIFFRACTION9A582 - 597
10X-RAY DIFFRACTION10A598 - 603
11X-RAY DIFFRACTION11B426 - 442
12X-RAY DIFFRACTION12B443 - 460
13X-RAY DIFFRACTION13B461 - 475
14X-RAY DIFFRACTION14B476 - 488
15X-RAY DIFFRACTION15B489 - 499
16X-RAY DIFFRACTION16B500 - 507
17X-RAY DIFFRACTION17B508 - 532
18X-RAY DIFFRACTION18B533 - 568
19X-RAY DIFFRACTION19B569 - 584
20X-RAY DIFFRACTION20B585 - 605
21X-RAY DIFFRACTION21C424 - 441
22X-RAY DIFFRACTION22C442 - 464
23X-RAY DIFFRACTION23C465 - 480
24X-RAY DIFFRACTION24C481 - 490
25X-RAY DIFFRACTION25C491 - 505
26X-RAY DIFFRACTION26C506 - 519
27X-RAY DIFFRACTION27C520 - 544
28X-RAY DIFFRACTION28C545 - 567
29X-RAY DIFFRACTION29C568 - 591
30X-RAY DIFFRACTION30C592 - 602
31X-RAY DIFFRACTION31D425 - 435
32X-RAY DIFFRACTION32D436 - 454
33X-RAY DIFFRACTION33D455 - 479
34X-RAY DIFFRACTION34D480 - 498
35X-RAY DIFFRACTION35D499 - 507
36X-RAY DIFFRACTION36D508 - 520
37X-RAY DIFFRACTION37D526 - 542
38X-RAY DIFFRACTION38D543 - 563
39X-RAY DIFFRACTION39D564 - 583
40X-RAY DIFFRACTION40D584 - 604

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