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- PDB-3i2t: Crystal structure of the unliganded Drosophila Epidermal Growth F... -

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Basic information

Entry
Database: PDB / ID: 3i2t
TitleCrystal structure of the unliganded Drosophila Epidermal Growth Factor Receptor ectodomain
ComponentsEpidermal growth factor receptor, isoform A
KeywordsTRANSFERASE / Drosophila / EGFR / ectodomain / unliganded / autoinhibited / ATP-binding / Nucleotide-binding / Tyrosine-protein kinase
Function / homology
Function and homology information


notum development / leg disc proximal/distal pattern formation / maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded / regulation of tube length, open tracheal system / wing and notum subfield formation / notum cell fate specification / R8 cell differentiation / Signaling by ERBB2 / Signaling by ERBB4 / SHC1 events in ERBB2 signaling ...notum development / leg disc proximal/distal pattern formation / maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded / regulation of tube length, open tracheal system / wing and notum subfield formation / notum cell fate specification / R8 cell differentiation / Signaling by ERBB2 / Signaling by ERBB4 / SHC1 events in ERBB2 signaling / PI3K events in ERBB4 signaling / Nuclear signaling by ERBB4 / Signaling by EGFR / EGFR interacts with phospholipase C-gamma / ERBB2 Regulates Cell Motility / Drug-mediated inhibition of ERBB2 signaling / oenocyte differentiation / dorsal closure, spreading of leading edge cells / maintenance of epithelial integrity, open tracheal system / lumen formation, open tracheal system / positive regulation of imaginal disc growth / stem cell fate commitment / photoreceptor cell fate determination / salivary gland development / imaginal disc development / photoreceptor cell differentiation / morphogenesis of follicular epithelium / epithelial cell proliferation involved in Malpighian tubule morphogenesis / PIP3 activates AKT signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / compound eye cone cell differentiation / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / Malpighian tubule morphogenesis / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / determination of genital disc primordium / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / RAF/MAP kinase cascade / tracheal outgrowth, open tracheal system / haltere development / compound eye photoreceptor cell differentiation / germ-band shortening / ommatidial rotation / negative regulation of compound eye retinal cell programmed cell death / Downregulation of ERBB4 signaling / EGFR downregulation / imaginal disc-derived wing vein morphogenesis / chorion-containing eggshell pattern formation / Cargo recognition for clathrin-mediated endocytosis / dorsal closure / establishment or maintenance of apical/basal cell polarity / spiracle morphogenesis, open tracheal system / wing disc morphogenesis / imaginal disc-derived wing vein specification / Clathrin-mediated endocytosis / dorsal appendage formation / border follicle cell migration / Estrogen-dependent gene expression / compound eye development / positive regulation of border follicle cell migration / segment polarity determination / imaginal disc-derived wing morphogenesis / oocyte axis specification / gonad development / germ-line stem cell population maintenance / behavioral response to ethanol / eye development / heart process / olfactory learning / embryonic pattern specification / peripheral nervous system development / establishment of epithelial cell apical/basal polarity / cell projection assembly / embryo development ending in birth or egg hatching / epidermal growth factor receptor activity / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of wound healing / negative regulation of apoptotic signaling pathway / positive regulation of cell division / positive regulation of phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / neurogenesis / basal plasma membrane / morphogenesis of an epithelium / determination of adult lifespan / epidermal growth factor receptor signaling pathway / receptor protein-tyrosine kinase / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / receptor complex
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / Receptor protein-tyrosine kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsAlvarado, D. / Klein, D.E. / Lemmon, M.A.
CitationJournal: Nature / Year: 2009
Title: ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor.
Authors: Alvarado, D. / Klein, D.E. / Lemmon, M.A.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification ..._pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0606
Polymers62,4521
Non-polymers2,6085
Water905
1
A: Epidermal growth factor receptor, isoform A
hetero molecules

A: Epidermal growth factor receptor, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,12012
Polymers124,9032
Non-polymers5,21710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7940 Å2
ΔGint58 kcal/mol
Surface area57090 Å2
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.378, 174.798, 161.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Non-polymers , 2 types, 6 molecules A

#1: Protein Epidermal growth factor receptor, isoform A


Mass: 62451.734 Da / Num. of mol.: 1 / Fragment: UNP residues 51-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Egfr / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q8MLW0, UniProt: P04412*PLUS, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAca1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Details

Sequence detailsAS PER AUTHOR THESE ARE ERRORS IN THE UNP DATABASE

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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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10% PEG 4,000, 0.1M HEPES, 5% Jeffamine M-600 (pH 7.0), 50mM KCl, 12.5% ethylene glycol, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91969 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91969 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 29225 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.083 / Χ2: 0.997 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.86.70.65728850.7661100
2.8-2.9170.46128490.7991100
2.91-3.047.30.32529060.8831100
3.04-3.27.10.22528861.0451100
3.2-3.47.20.1529240.7491100
3.4-3.667.10.10629120.9321100
3.66-4.037.10.08429091.2341100
4.03-4.6270.07229371.6471100
4.62-5.8170.06129761.7931100
5.81-456.70.04930410.09198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.81 Å36.76 Å
Translation2.81 Å36.76 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29198
Phasing dm shell
Resolution (Å)Delta phi finalReflectionFOM
10.52-10080.4503
8.42-10.5254.95050.645
7.3-8.4250.15400.704
6.53-7.3526070.681
5.97-6.5353.86580.686
5.53-5.9754.57230.691
5.17-5.5351.77790.729
4.88-5.1746.28070.749
4.63-4.8846.48670.743
4.41-4.6349.59000.746
4.22-4.4146.79340.782
4.06-4.2250.39770.769
3.91-4.0649.710150.725
3.78-3.9150.810410.748
3.66-3.785010860.7
3.55-3.6652.111120.743
3.45-3.5552.311620.725
3.36-3.4552.611600.746
3.27-3.3655.412070.712
3.2-3.2758.712490.693
3.12-3.259.812460.695
3.05-3.1260.413100.676
2.99-3.056213290.696
2.93-2.9959.713490.695
2.87-2.935913520.666
2.82-2.8760.614230.674
2.77-2.8261.314200.662
2.7-2.7762.219370.604

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2a91

2a91


Resolution: 2.7→36.68 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.334 / WRfactor Rwork: 0.318 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.798 / SU B: 26.801 / SU ML: 0.242 / SU R Cruickshank DPI: 0.768 / SU Rfree: 0.417 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.55 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2654 10.1 %RANDOM
Rwork0.224 ---
obs0.228 26324 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.65 Å2 / Biso mean: 48.965 Å2 / Biso min: 25.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å20 Å2
2--0.27 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 173 5 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214500
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9916127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45824.39205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41215699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8841525
X-RAY DIFFRACTIONr_chiral_restr0.1060.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213379
X-RAY DIFFRACTIONr_mcbond_it0.5141.52694
X-RAY DIFFRACTIONr_mcangle_it1.05224336
X-RAY DIFFRACTIONr_scbond_it1.64431806
X-RAY DIFFRACTIONr_scangle_it2.7364.51791
LS refinement shellResolution: 2.7→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 224 -
Rwork0.366 1696 -
all-1920 -
obs--99.95 %
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)
13.14060.62280.54414.78380.47883.89690.0917-0.15310.3792-0.04280.0819-0.1018-0.1941-0.2473-0.17360.01470.00650.02570.0242-0.00920.0658-24.7736-21.3158-7.9961
21.1406-0.98640.31430.8626-0.36592.31040.10150.08420.0831-0.1046-0.0488-0.0633-0.2107-0.0758-0.05270.1469-0.00610.00030.28480.04720.0146-31.0077-33.6003-35.3061
35.0866-0.1568-0.53053.32420.11752.3644-0.1080.1021-0.63680.1048-0.0394-0.21330.35610.21810.14740.0560.03070.01940.0254-0.00150.0993-26.4841-59.5635-11.4226
42.19063.44233.36587.05715.04335.20910.1985-0.128-0.0056-0.1073-0.20430.00770.3691-0.21250.00580.46630.09290.11070.5898-0.0820.5348-20.0964-82.6584-34.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 203
2X-RAY DIFFRACTION2A204 - 303
3X-RAY DIFFRACTION3A304 - 491
4X-RAY DIFFRACTION4A492 - 550

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