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- PDB-2wqz: Crystal structure of synaptic protein neuroligin-4 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2wqz
TitleCrystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement
Components
  • NEUREXIN-1-BETA
  • NEUROLIGIN 4, X-LINKED
KeywordsCELL ADHESION / TRANSMEMBRANE / DISULFIDE BOND / ALPHA/BETA-HYDROLASE CHOLINESTERASE AUTISM BRAIN / ALTERNATIVE PROMOTER USAGE / MEMBRANE / GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of protein kinase A signaling / asymmetric, glutamatergic, excitatory synapse / protein-containing complex assembly involved in synapse maturation / symmetric, GABA-ergic, inhibitory synapse / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / gephyrin clustering involved in postsynaptic density assembly / type 1 fibroblast growth factor receptor binding / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission ...positive regulation of protein kinase A signaling / asymmetric, glutamatergic, excitatory synapse / protein-containing complex assembly involved in synapse maturation / symmetric, GABA-ergic, inhibitory synapse / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / gephyrin clustering involved in postsynaptic density assembly / type 1 fibroblast growth factor receptor binding / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / cerebellar granule cell differentiation / trans-synaptic signaling, modulating synaptic transmission / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / negative regulation of filopodium assembly / synapse maturation / maintenance of synapse structure / vocal learning / slit diaphragm / neuroligin family protein binding / positive regulation of synapse maturation / neuron cell-cell adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic vesicle clustering / brainstem development / regulation of grooming behavior / neurexin family protein binding / inhibitory synapse / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / receptor localization to synapse / presynapse assembly / negative regulation of excitatory postsynaptic potential / NMDA glutamate receptor clustering / vocalization behavior / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / protein localization to synapse / regulation of postsynaptic density assembly / neurotransmitter secretion / filopodium assembly / cell-cell junction organization / neuron maturation / acetylcholine receptor binding / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / regulation of synaptic vesicle cycle / NMDA selective glutamate receptor signaling pathway / postsynaptic specialization membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Neurexins and neuroligins / chloride ion binding / organ growth / regulation of synapse assembly / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / adult behavior / social behavior / neuromuscular process controlling balance / synaptic vesicle endocytosis / positive regulation of excitatory postsynaptic potential / excitatory synapse / regulation of presynapse assembly / endocytic vesicle / calcium channel regulator activity / prepulse inhibition / axonal growth cone / synapse assembly / cell adhesion molecule binding / presynaptic active zone membrane / cerebellum development / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / GABA-ergic synapse / learning / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / modulation of chemical synaptic transmission / synapse organization / establishment of protein localization / postsynaptic density membrane / neuromuscular junction / Schaffer collateral - CA1 synapse / neuron differentiation / positive regulation of neuron projection development / circadian rhythm / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / signaling receptor activity / presynapse / presynaptic membrane / scaffold protein binding / nuclear membrane / angiogenesis
Similarity search - Function
Neuroligin / Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain ...Neuroligin / Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Jelly Rolls - #200 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neurexin-1-beta / Neuroligin-4, X-linked
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsFabrichny, I.P. / Leone, P. / Sulzenbacher, G. / Comoletti, D. / Miller, M.T. / Taylor, P. / Bourne, Y. / Marchot, P.
CitationJournal: Neuron / Year: 2007
Title: Structural Analysis of the Synaptic Protein Neuroligin and its Beta-Neurexin Complex: Determinants for Folding and Cell Adhesion.
Authors: Fabrichny, I.P. / Leone, P. / Sulzenbacher, G. / Comoletti, D. / Miller, M.T. / Taylor, P. / Bourne, Y. / Marchot, P.
History
DepositionAug 28, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionSep 8, 2009ID: 2VH8
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 24, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROLIGIN 4, X-LINKED
B: NEUROLIGIN 4, X-LINKED
C: NEUREXIN-1-BETA
D: NEUREXIN-1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,7188
Polymers171,1964
Non-polymers5234
Water00
1
A: NEUROLIGIN 4, X-LINKED
D: NEUREXIN-1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0805
Polymers85,5982
Non-polymers4823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NEUROLIGIN 4, X-LINKED
C: NEUREXIN-1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6383
Polymers85,5982
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.520, 198.670, 85.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALALEULEU4AA41 - 6210 - 31
211ALAALALEULEU4BB41 - 6210 - 31
121PROPROCYSCYS4AA69 - 11038 - 79
221PROPROCYSCYS4BB69 - 11038 - 79
131ASNASNTYRTYR4AA143 - 407112 - 376
231ASNASNTYRTYR4BB143 - 407112 - 376
141ASPASPHISHIS4AA414 - 598383 - 567
241ASPASPHISHIS4BB414 - 598383 - 567
112HISHISVALVAL6CC82 - 2883 - 179
212HISHISVALVAL6DD82 - 2883 - 179

NCS ensembles :
ID
1
2

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Components

#1: Protein NEUROLIGIN 4, X-LINKED / NEUROLIGIN X / HNLX / NEUROLIGIN 4


Mass: 66230.203 Da / Num. of mol.: 2 / Fragment: ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8N0W4
#2: Protein NEUREXIN-1-BETA / NEUREXIN I-BETA / BETA-NEUREXIN 1


Mass: 19367.713 Da / Num. of mol.: 2 / Fragment: LNS DOMAIN, RESIDUES 80-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q63373
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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: 4.24 Å3/Da / Density % sol: 70.8 % / Description: NONE
Crystal growpH: 6.5 / Details: 8% PEG 20000, 0.1M MES PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.9→30 Å / Num. obs: 25251 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 3.9→4 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3BE8 AND 1C4R

3be8

1c4r


Resolution: 3.9→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / SU B: 107.112 / SU ML: 0.634 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.754 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1261 5 %RANDOM
Rwork0.205 ---
obs0.208 23955 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2--1.97 Å20 Å2
3----4.42 Å2
Refinement stepCycle: LAST / Resolution: 3.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11330 0 30 0 11360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211652
X-RAY DIFFRACTIONr_bond_other_d0.0030.027685
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.94815870
X-RAY DIFFRACTIONr_angle_other_deg0.964318751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.92151434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61824.595555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.169151825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8431554
X-RAY DIFFRACTIONr_chiral_restr0.0810.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022340
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_it0.2651.57162
X-RAY DIFFRACTIONr_mcbond_other0.0311.52926
X-RAY DIFFRACTIONr_mcangle_it0.505211575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.51834490
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9354.54295
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6558medium positional0.580.5
12B6558medium positional0.580.5
21C2284loose positional0.695
22D2284loose positional0.695
11A6558medium thermal0.192
12B6558medium thermal0.192
21C2284loose thermal2.4210
22D2284loose thermal2.4210
LS refinement shellResolution: 3.9→4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 90 -
Rwork0.351 1708 -
obs--100 %
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)
13.40870.566-0.19844.75590.64532.7718-0.1461-0.122-0.2798-0.1501-0.00440.24690.67320.45920.15050.74290.34620.02740.9095-0.04790.134216.921-27.962-22.967
21.60480.6614.97441.28143.377517.4789-0.0338-0.183-0.18681.29820.4799-0.01281.42670.7992-0.4461.81880.34430.04021.66650.24180.717824.317-28.193-3.251
32.50740.01031.034214.431.77921.6264-0.2819-0.7186-0.64030.57850.8047-0.91520.46110.3944-0.52281.11280.6648-0.18941.5468-0.00020.649641.916-35.176-12.789
42.386-0.3204-1.422710.65771.55347.58020.1149-0.50920.2596-0.03850.0884-1.2435-0.23730.9898-0.20340.52790.0308-0.02571.3331-0.17380.221133.13-1.957-8.574
52.89714.0361-1.26657.25141.58287.88240.205-0.50950.2750.6509-0.68140.74350.2661-0.20730.47640.67230.3120.05830.9139-0.08780.45868.222-15.334-11.919
63.12431.15670.50524.891-0.26952.6647-0.41550.61571.0476-0.30230.18840.1987-0.6450.36130.22720.9559-0.32830.00011.07020.31630.703735.9744.926-9.784
711.61485.82678.56143.47456.16213.3244-0.1439-0.20840.7209-0.5226-0.11150.2169-0.70350.47660.25542.1428-0.10760.43521.76740.51331.173137.77842.657-30.574
84.673-2.2472-4.04411.50792.24783.7246-0.38630.33450.2952-0.08380.6924-0.56260.17710.26-0.30611.3321-0.61160.40932.21850.30291.190558.32441.003-26.196
92.3971.79121.8228.5945-0.80286.9745-0.04921.1385-0.1969-0.78620.079-0.72920.09250.9092-0.02981.0246-0.20060.29111.58310.00420.25735.45115.232-25.278
101.7031-2.7991.52925.8026-1.58183.26430.1520.6180.1203-0.9769-0.50670.7353-0.86610.35370.35481.1597-0.3895-0.12811.29440.48850.99720.1737.877-17.834
118.64910.1871-1.03853.88311.4078.01250.1207-0.29550.03030.85910.0575-0.08840.0819-0.5901-0.17821.0191-0.17760.18930.6880.27320.577144.82234.74524.502
123.49262.33211.16262.4429-0.24218.4211-0.23061.3767-0.2489-0.91790.22820.15690.4506-0.13250.00241.59710.4487-0.11521.7505-0.15230.463422.314-18.18-58.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 110
2X-RAY DIFFRACTION1A143 - 291
3X-RAY DIFFRACTION1A340 - 373
4X-RAY DIFFRACTION1A449 - 472
5X-RAY DIFFRACTION1A561 - 582
6X-RAY DIFFRACTION2A111 - 142
7X-RAY DIFFRACTION3A292 - 339
8X-RAY DIFFRACTION4A374 - 448
9X-RAY DIFFRACTION4A583 - 598
10X-RAY DIFFRACTION5A473 - 560
11X-RAY DIFFRACTION6B41 - 110
12X-RAY DIFFRACTION6B143 - 291
13X-RAY DIFFRACTION6B340 - 373
14X-RAY DIFFRACTION6B449 - 472
15X-RAY DIFFRACTION6B561 - 582
16X-RAY DIFFRACTION7B111 - 142
17X-RAY DIFFRACTION8B292 - 339
18X-RAY DIFFRACTION9B374 - 448
19X-RAY DIFFRACTION9B583 - 599
20X-RAY DIFFRACTION10B473 - 560
21X-RAY DIFFRACTION11C82 - 288
22X-RAY DIFFRACTION12D82 - 288

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