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- PDB-4en2: HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adapti... -

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Basic information

Entry
Database: PDB / ID: 4en2
TitleHIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)
Components
  • AP-1 complex subunit mu-1
  • MHC-I
  • Protein Nef
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Human immunodeficiency virus 1 / HIV / Nef / MHC-I / antigen presentation / host defense / Adaptor protein complex 1 / Mu1 adaptin subunit / sorting motif recognition / CLASP / membrane trafficking / viral hijacking / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / protein trimerization / platelet dense granule organization / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis ...: / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / protein trimerization / platelet dense granule organization / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host autophagy / MHC class II antigen presentation / CD4 receptor binding / thioesterase binding / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / MHC class I protein binding / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / vesicle-mediated transport / regulation of calcium-mediated signaling / viral life cycle / Neutrophil degranulation / Nef mediated downregulation of MHC class I complex cell surface expression / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / virion component / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / Interferon alpha/beta signaling / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / ATPase binding / ER-Phagosome pathway / early endosome membrane / early endosome / defense response to Gram-positive bacterium / immune response / symbiont-mediated suppression of host innate immune response / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / synapse / endoplasmic reticulum membrane / protein kinase binding / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / Mu homology domain, subdomain B / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site ...Nef Regulatory Factor / Nef Regulatory Factor / Mu homology domain, subdomain B / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / AP-1 complex subunit mu-1 / Protein Nef
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsJia, X. / Xiong, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef.
Authors: Jia, X. / Singh, R. / Homann, S. / Yang, H. / Guatelli, J. / Xiong, Y.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: AP-1 complex subunit mu-1
B: Protein Nef
C: Protein Nef
A: AP-1 complex subunit mu-1
D: MHC-I
E: MHC-I


Theoretical massNumber of molelcules
Total (without water)113,5216
Polymers113,5216
Non-polymers00
Water95553
1
M: AP-1 complex subunit mu-1
C: Protein Nef
D: MHC-I


Theoretical massNumber of molelcules
Total (without water)56,7603
Polymers56,7603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-15 kcal/mol
Surface area19970 Å2
MethodPISA
2
B: Protein Nef
A: AP-1 complex subunit mu-1
E: MHC-I


Theoretical massNumber of molelcules
Total (without water)56,7603
Polymers56,7603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-12 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.033, 98.128, 112.740
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
11M
21A
12B
22C
13D
23E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHRMA160 - 4223 - 265
21ARGARGTHRTHRAD160 - 4223 - 265
12SERSERPHEPHEBB9 - 2039 - 203
22SERSERPHEPHECC9 - 2039 - 203
13SERSERALAALADE319 - 3296 - 16
23SERSERALAALAEF319 - 3296 - 16

NCS ensembles :
ID
1
2
3

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Components

#1: Protein AP-1 complex subunit mu-1 / AP-mu chain family member mu1A / Adaptor protein complex AP-1 mu-1 subunit / Adaptor-related ...AP-mu chain family member mu1A / Adaptor protein complex AP-1 mu-1 subunit / Adaptor-related protein complex 1 mu-1 subunit / Clathrin assembly protein complex 1 medium chain 1 / Clathrin coat assembly protein AP47 / Clathrin coat-associated protein AP47 / Golgi adaptor HA1/AP1 adaptin mu-1 subunit / Mu-adaptin 1 / Mu1A-adaptin


Mass: 30612.102 Da / Num. of mol.: 2 / Fragment: sorting motif recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Production host: Escherichia coli (E. coli) / References: UniProt: P35585
#2: Protein Protein Nef


Mass: 23399.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL-43 / Gene: nef / Production host: Escherichia coli (E. coli) / References: UniProt: Q90VU7
#3: Protein/peptide MHC-I


Mass: 2748.915 Da / Num. of mol.: 2 / Fragment: cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04439*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 298 K / Method: microbatch underoil / pH: 6.5
Details: 0.1M HEPES, 3% PEG8000, pH 6.5, microbatch underoil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 31023 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.58-2.693.8199.6
2.69-2.84199.90.948
2.8-2.93411000.676
2.93-3.08411000.449
3.08-3.28411000.273
3.28-3.53411000.171
3.53-3.883.911000.103
3.88-4.453.8199.80.072
4.45-5.63.7199.80.052
5.6-503.6199.20.04

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→48.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.39 / SU B: 28.523 / SU ML: 0.276 / SU R Cruickshank DPI: 0.5039 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25843 1561 5.1 %RANDOM
Rwork0.20771 ---
obs0.21022 29309 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.793 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2--2.53 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.58→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6721 0 0 53 6774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196908
X-RAY DIFFRACTIONr_bond_other_d0.0060.026578
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.959341
X-RAY DIFFRACTIONr_angle_other_deg1.083315138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92522.955335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.327151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4521559
X-RAY DIFFRACTIONr_chiral_restr0.0850.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217681
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021666
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11M9108X-RAY DIFFRACTIONLOCAL
12A9108X-RAY DIFFRACTIONLOCAL
21B4894X-RAY DIFFRACTIONLOCAL
22C4894X-RAY DIFFRACTIONLOCAL
31D188X-RAY DIFFRACTIONLOCAL
32E188X-RAY DIFFRACTIONLOCAL
LS refinement shellResolution: 2.58→2.648 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 82 -
Rwork0.344 1767 -
obs--81.92 %
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)
11.06830.24571.28551.1413-0.55122.32920.1228-0.29610.02070.0068-0.0324-0.00520.0072-0.3966-0.09040.31380.06360.04670.45980.0180.2841-41.136-16.632-2.95
21.3832-0.6819-0.22532.04520.49082.17930.0391-0.0893-0.1223-0.1074-0.00530.08810.045-0.5654-0.03380.2997-0.0351-0.02340.33570.02490.254-45.703-21.622-12.511
31.88650.41581.39721.3730.01724.7872-0.0027-0.65370.1470.1741-0.0117-0.15880.0278-0.13470.01440.2522-0.00940.01220.6183-0.07130.2521-22.052-17.06916.94
41.3096-0.2251.91720.6698-0.60013.69840.0909-0.33920.0714-0.1010.19810.11270.0612-0.5042-0.2890.3707-0.01350.0260.36830.02810.3048-38.413-14.864-7.694
56.2089-3.117-0.484311.6231-7.42237.3796-0.23470.35250.59970.2322-0.2242-1.0167-0.4730.69980.45890.3221-0.1339-0.060.3849-0.07840.3836-12.145-16.746-24.757
62.2859-1.7468-0.64053.06480.92210.30570.01430.01490.188-0.1262-0.04840.1851-0.11430.01860.03410.4327-0.09380.07310.27670.00860.2923-27.332-13.886-20.993
72.3345-0.76490.34062.56861.28420.9033-0.04220.0883-0.0664-0.12030.1601-0.0819-0.12960.1047-0.1180.3979-0.03480.05230.3029-0.00140.257-22.72-24.343-28.097
811.1939-3.9779-0.58147.42030.47090.04340.64690.8554-1.0359-0.722-0.64310.5075-0.0453-0.0354-0.00390.34860.1914-0.05730.5717-0.18830.2814-20.512-39.843-38.084
90.30940.1314-0.69770.5553-0.79236.46030.06130.3482-0.0893-0.2414-0.01290.07770.1053-0.3774-0.04840.42980.0521-0.00270.5201-0.10020.2884-30.477-28.545-35.346
1023.57944.335721.921726.17216.845420.69480.66442.9868-2.6135-2.64771.63780.42690.32282.9189-2.30221.5041-0.41560.39361.2296-0.44250.6712-23.055-24.92247.956
1111.7953-3.814912.48541.2778-3.672517.09520.2095-1.8172-2.1280.00420.67080.87170.3798-0.4841-0.88030.5422-0.17510.19231.68490.2541.2191-17.912-11.74532.065
124.34194.5083-3.40714.8267-5.346130.2548-0.28960.033-0.4512-0.40350.0395-0.35941.2796-0.30170.250.24440.1519-0.09590.20330.00380.4529-41.903-10.53739.618
136.28621.9678-0.90153.7815-2.12713.1369-0.61740.7285-0.2161-0.52030.51780.06410.77240.02460.09960.5351-0.04610.04330.4211-0.03180.1501-26.49-17.58453.717
143.57740.2992-0.16094.571-1.50340.8764-0.11580.08540.12540.26950.11410.0316-0.03970.30920.00160.35140.0076-0.02690.47060.04210.2104-22.805-8.20859.955
1527.58813.406612.17850.63832.848115.09330.1973-0.6976-0.15220.0472-0.1574-0.14120.337-0.6419-0.03990.3032-0.0424-0.0260.12070.12710.5185-46.079-7.59552.838
161.6067-1.703-0.56473.7895.63213.8983-0.02310.43950.2967-0.1335-0.1865-0.1093-0.16650.20570.20950.3964-0.03580.03060.40240.07520.3472-37.583-11.963-18.197
173.75951.2316-2.89320.419-1.18176.4705-0.04370.1102-0.2044-0.02060.066-0.060.0232-0.025-0.02230.30030.00250.01340.3852-0.04290.2923-51.643.56544.708
183.96270.1741-0.63671.9756-0.33750.6132-0.0485-0.1308-0.0632-0.00690.0132-0.1050.0229-0.06440.03530.315-0.0259-0.04570.2471-0.04270.2728-40.8386.96949.517
199.637-1.733611.10520.3723-1.267822.18450.24341.2547-0.0807-0.0419-0.16110.0189-0.0682.0186-0.08220.407-0.01990.03660.3759-0.04460.2028-48.716-0.8318.037
202.2346-1.24822.40842.1438-3.07437.53370.06910.2648-0.0084-0.14430.0537-0.0030.41730.3627-0.12280.3038-0.05910.00110.3301-0.0510.2901-53.745-2.75416.125
211.90410.6509-0.48160.253-0.34966.03220.04930.128-0.17420.10840.0402-0.103-0.13290.1835-0.08950.36820.0246-0.05130.2673-0.04280.3646-47.719-1.26643.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A160 - 198
2X-RAY DIFFRACTION2A199 - 271
3X-RAY DIFFRACTION3A272 - 382
4X-RAY DIFFRACTION4A383 - 423
5X-RAY DIFFRACTION5B6 - 24
6X-RAY DIFFRACTION6B64 - 90
7X-RAY DIFFRACTION7B91 - 148
8X-RAY DIFFRACTION8B149 - 178
9X-RAY DIFFRACTION9B179 - 204
10X-RAY DIFFRACTION10C12 - 21
11X-RAY DIFFRACTION11C22 - 62
12X-RAY DIFFRACTION12C63 - 77
13X-RAY DIFFRACTION13C78 - 117
14X-RAY DIFFRACTION14C118 - 203
15X-RAY DIFFRACTION15D319 - 329
16X-RAY DIFFRACTION16E317 - 331
17X-RAY DIFFRACTION17M158 - 208
18X-RAY DIFFRACTION18M209 - 273
19X-RAY DIFFRACTION19M274 - 294
20X-RAY DIFFRACTION20M295 - 381
21X-RAY DIFFRACTION21M382 - 423

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