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- PDB-2uwe: Large CDR3a loop alteration as a function of MHC mutation -

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Basic information

Entry
Database: PDB / ID: 2uwe
TitleLarge CDR3a loop alteration as a function of MHC mutation
Components
  • AHIII TCR ALPHA CHAIN
  • AHIII TCR BETA CHAIN
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
  • UNCHARACTERIZED PROTEIN C15ORF24
KeywordsIMMUNE SYSTEM / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / GLYCOPROTEIN / TRANSMEMBRANE / MHC I / MEMBRANE / RECEPTOR / CLASS I MHC / HYPOTHETICAL PROTEIN / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN / IMMUNE RESPONSE / TCR-PMHC COMPLEX / T CELL SIGNALING / DISEASE MUTATION
Function / homology
Function and homology information


EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / tail-anchored membrane protein insertion into ER membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / tail-anchored membrane protein insertion into ER membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / carbohydrate binding / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / : / Carbohydrate-binding-like fold / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / : / Carbohydrate-binding-like fold / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / T-cell receptor beta chain V region C5 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Endoplasmic reticulum membrane protein complex subunit 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMiller, P.J. / Pazy, Y. / Conti, B. / Riddle, D. / Biddison, W.E. / Appella, E. / Collins, E.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Single Mhc Mutation Eliminates Enthalpy Associated with T Cell Receptor Binding.
Authors: Miller, P.J. / Pazy, Y. / Conti, B. / Riddle, D. / Appella, E. / Collins, E.J.
History
DepositionMar 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: UNCHARACTERIZED PROTEIN C15ORF24
E: AHIII TCR ALPHA CHAIN
F: AHIII TCR BETA CHAIN
H: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
I: BETA-2-MICROGLOBULIN
J: UNCHARACTERIZED PROTEIN C15ORF24
L: AHIII TCR ALPHA CHAIN
M: AHIII TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)186,60010
Polymers186,60010
Non-polymers00
Water3,783210
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: UNCHARACTERIZED PROTEIN C15ORF24
E: AHIII TCR ALPHA CHAIN
F: AHIII TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)93,3005
Polymers93,3005
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-77.5 kcal/mol
Surface area46230 Å2
MethodPQS
2
H: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
I: BETA-2-MICROGLOBULIN
J: UNCHARACTERIZED PROTEIN C15ORF24
L: AHIII TCR ALPHA CHAIN
M: AHIII TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)93,3005
Polymers93,3005
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-79 kcal/mol
Surface area46140 Å2
MethodPQS
Unit cell
Length a, b, c (Å)93.489, 84.178, 121.773
Angle α, β, γ (deg.)90.00, 92.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AHBIELFM

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN / HLA-A201 / MHC CLASS I ANTIGEN A*2


Mass: 31824.176 Da / Num. of mol.: 2 / Fragment: ECTO-DOMAIN, RESIDUES 25-299 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MUTATION OF HLA-A2.1 AT POSITION 163, THREONINE TO ALANINE
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: T163A / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Details: HAS EXTRA METHIONINE DUE TO ESCHERICHIA COLI EXPRESSION
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P61769
#4: Protein AHIII TCR ALPHA CHAIN


Mass: 21656.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: B6 / Cell: T CELL / Cell line: AHIII T CELL CLONE / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL
#5: Protein AHIII TCR BETA CHAIN


Mass: 26890.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: B6 / Cell: T CELL / Cell line: AHIII T CELL CLONE / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P04213*PLUS

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Protein/peptide / Non-polymers , 2 types, 212 molecules CJ

#3: Protein/peptide UNCHARACTERIZED PROTEIN C15ORF24 / SELF-PEPTIDE / P1049


Mass: 1049.263 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-12 / Source method: obtained synthetically
Details: SELF-PEPTIDE RECOGNIZED BY AHIII T CELL WHEN PRESENTED BY HLA-A2.1.
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NPA0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 187 TO ALA ENGINEERED RESIDUE IN CHAIN H, THR 187 TO ALA
Has protein modificationY
Sequence detailsMUTANT T163A ADDITIONAL METHIONINE AT N-TERMINUS DUE TO EXPRESSION IN E. COLI

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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: 2.55 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.8 / Details: 14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 76682 / % possible obs: 83.9 % / Observed criterion σ(I): 0 / Redundancy: 2.76 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 2.37→2.49 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.64 / % possible all: 67.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LP9

1lp9


Resolution: 2.4→121 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 21.998 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.846 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 52-58 IN THE TCR CHAINS E AND L ARE COMPLETELY DISORDERED AND THUS HAVE AN OCCUPANCY OF 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3142 5 %RANDOM
Rwork0.24 ---
obs0.243 59694 84.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.28 Å2
2--0.86 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13140 0 0 210 13350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02113324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.92918109
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11751603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83223.57647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.284152137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4171582
X-RAY DIFFRACTIONr_chiral_restr0.0580.21911
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.25008
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.28751
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3011.58329
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.377213001
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.53535880
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.794.55108
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
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 187 -
Rwork0.338 3469 -
obs--67.23 %
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)
12.01160.51880.14953.32610.80372.28220.0646-0.0798-0.0825-0.0878-0.0243-0.00290.0247-0.127-0.0404-0.17750.04120.0472-0.18350.0453-0.218915.979-1.82419.663
21.4929-0.2188-0.4384.2927-3.31026.66830.139-0.3246-0.2561-0.2017-0.0885-0.02140.28360.0492-0.0506-0.03430.0539-0.001-0.05490.0045-0.075312.739-2.57154.655
32.6109-1.0703-1.14634.65923.88835.107-0.1211-0.06110.03750.2513-0.05970.41510.1069-0.53820.1807-0.09380.03450.01660.05640.0583-0.1652-1.1265.58238.988
42.0403-0.3851-0.22630.807-0.34671.5434-0.00130.0694-0.021-0.0037-0.0060.072-0.1483-0.04820.0072-0.0783-0.01380.0388-0.1257-0.0062-0.141626.3540.493-7.443
53.8007-1.6613-0.31143.18710.68132.17970.10630.31030.1742-0.0986-0.1225-0.1178-0.17810.19660.0161-0.0984-0.0527-0.02530.06150.0509-0.105633.7880.43-38.773
62.59510.1418-0.14232.97980.612.8943-0.0065-0.0563-0.0245-0.0298-0.0140.01850.2233-0.20740.0205-0.2079-0.01950.0567-0.18010.021-0.216716.15440.69424.561
72.00160.384-0.68024.5406-4.50918.02160.0667-0.1579-0.2191-0.02340.1116-0.05850.3119-0.0077-0.1784-0.09250.0363-0.0049-0.1004-0.0471-0.064413.19839.6159.718
83.0614-0.5609-1.12224.59753.30765.5102-0.08660.08460.11910.20530.09440.25430.0751-0.3904-0.0078-0.17750.00260.0206-0.0320.0852-0.154-0.81948.23344.076
91.8758-0.5827-0.19960.7828-0.47092.06-0.06050.0611-0.0718-0.05890.04890.071-0.1216-0.13520.0117-0.1119-0.04240.0323-0.1377-0.0193-0.137626.62242.896-2.493
104.3365-2.2185-0.31552.98270.182.24470.22940.29810.1034-0.2303-0.1948-0.1018-0.28380.2048-0.0345-0.0084-0.0349-0.04280.0627-0.0059-0.084134.31743.6-33.689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 183
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A184 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4E0 - 116
6X-RAY DIFFRACTION4F1 - 116
7X-RAY DIFFRACTION5E117 - 198
8X-RAY DIFFRACTION5F117 - 245
9X-RAY DIFFRACTION6H1 - 183
10X-RAY DIFFRACTION6J1 - 9
11X-RAY DIFFRACTION7H184 - 275
12X-RAY DIFFRACTION8I0 - 99
13X-RAY DIFFRACTION9L0 - 116
14X-RAY DIFFRACTION9M1 - 116
15X-RAY DIFFRACTION10L117 - 198
16X-RAY DIFFRACTION10M117 - 245

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