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- PDB-6m4x: Co-crystal structure of Ac-AChBPP in complex with [N9A]LvIA -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6m4x
TitleCo-crystal structure of Ac-AChBPP in complex with [N9A]LvIA
Components
  • Alpha-conotoxin LvIA
  • Soluble acetylcholine receptor
KeywordsMETAL BINDING PROTEIN/TOXIN / complex / conotoxin / AChBP / ion channel / METAL BINDING PROTEIN-TOXIN complex
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / toxin activity / neuron projection / synapse / extracellular region ...host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / toxin activity / neuron projection / synapse / extracellular region / membrane / identical protein binding / metal ion binding
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Alpha-conotoxin LvIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus lividus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å
AuthorsWang, X.Q. / Pan, S. / Luo, S.L. / Zhu, X.P.
CitationJournal: To Be Published
Title: The crystal structure of Ac-AChBP in complex with LvIA analogs reveals the mechanism of its selectivity towards different nAChR subtypes
Authors: Zhu, X.P. / Pan, S. / Wang, X.Q. / Luo, S.L.
History
DepositionMar 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / 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
A: Soluble acetylcholine receptor
F: Alpha-conotoxin LvIA
B: Soluble acetylcholine receptor
C: Alpha-conotoxin LvIA
D: Soluble acetylcholine receptor
E: Alpha-conotoxin LvIA
G: Soluble acetylcholine receptor
H: Alpha-conotoxin LvIA
I: Soluble acetylcholine receptor
J: Alpha-conotoxin LvIA


Theoretical massNumber of molelcules
Total (without water)125,88610
Polymers125,88610
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-115 kcal/mol
Surface area43910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.441, 207.441, 114.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:13 or resseq 15:16 or (resid...
21(chain B and (resseq 1:13 or resseq 15:16 or (resid...
31(chain D and (resseq 1:13 or resseq 15:16 or (resid...
41(chain G and (resseq 1:13 or resseq 15:16 or (resid...
51(chain I and (resseq 1:13 or resseq 15:16 or (resid...
12(chain E and (resseq 401:410 or (resid 411 and (name...
22(chain C and (resseq 401:410 or (resid 411 and (name...
32(chain F and (resseq 401:410 or (resid 411 and (name...
42(chain H and (resseq 401:410 or (resid 411 and (name...
52(chain J and (resseq 401:410 or (resid 411 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNASNASN(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA1 - 132 - 14
121SERSERPROPRO(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA15 - 1616 - 17
131SERSERSERSER(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA01
141SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
151SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
161SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
171SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
181SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
191SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
1101SERSERARGARG(chain A and (resseq 1:13 or resseq 15:16 or (resid...AA0 - 2061 - 207
211GLNGLNASNASN(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC1 - 132 - 14
221SERSERPROPRO(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC15 - 1616 - 17
231SERSERSERSER(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC01
241SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
251SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
261SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
271SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
281SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
291SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
2101SERSERARGARG(chain B and (resseq 1:13 or resseq 15:16 or (resid...BC0 - 2061 - 207
311GLNGLNASNASN(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE1 - 132 - 14
321SERSERPROPRO(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE15 - 1616 - 17
331TYRTYRTYRTYR(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE1819
341SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
351SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
361SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
371SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
381SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
391SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
3101SERSERARGARG(chain D and (resseq 1:13 or resseq 15:16 or (resid...DE0 - 2061 - 207
411GLNGLNASNASN(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG1 - 132 - 14
421SERSERPROPRO(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG15 - 1616 - 17
431SERSERSERSER(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG01
441SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
451SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
461SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
471SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
481SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
491SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
4101SERSERARGARG(chain G and (resseq 1:13 or resseq 15:16 or (resid...GG0 - 2061 - 207
511GLNGLNASNASN(chain I and (resseq 1:13 or resseq 15:16 or (resid...II1 - 132 - 14
521SERSERPROPRO(chain I and (resseq 1:13 or resseq 15:16 or (resid...II15 - 1616 - 17
531TYRTYRTYRTYR(chain I and (resseq 1:13 or resseq 15:16 or (resid...II1819
541SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
551SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
561SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
571SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
581SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
591SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
5101SERSERARGARG(chain I and (resseq 1:13 or resseq 15:16 or (resid...II0 - 2061 - 207
112GLYGLYVALVAL(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4101 - 10
122ASPASPASPASP(chain E and (resseq 401:410 or (resid 411 and (name...EF41111
132GLYGLYNH2NH2(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4171 - 17
142GLYGLYNH2NH2(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4171 - 17
152GLYGLYNH2NH2(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4171 - 17
162GLYGLYNH2NH2(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4171 - 17
172GLYGLYNH2NH2(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4171 - 17
182GLYGLYNH2NH2(chain E and (resseq 401:410 or (resid 411 and (name...EF401 - 4171 - 17
212GLYGLYVALVAL(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4101 - 10
222ASPASPASPASP(chain C and (resseq 401:410 or (resid 411 and (name...CD41111
232GLYGLYNH2NH2(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4171 - 17
242GLYGLYNH2NH2(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4171 - 17
252GLYGLYNH2NH2(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4171 - 17
262GLYGLYNH2NH2(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4171 - 17
272GLYGLYNH2NH2(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4171 - 17
282GLYGLYNH2NH2(chain C and (resseq 401:410 or (resid 411 and (name...CD401 - 4171 - 17
312GLYGLYVALVAL(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4101 - 10
322ASPASPASPASP(chain F and (resseq 401:410 or (resid 411 and (name...FB41111
332GLYGLYNH2NH2(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4171 - 17
342GLYGLYNH2NH2(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4171 - 17
352GLYGLYNH2NH2(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4171 - 17
362GLYGLYNH2NH2(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4171 - 17
372GLYGLYNH2NH2(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4171 - 17
382GLYGLYNH2NH2(chain F and (resseq 401:410 or (resid 411 and (name...FB401 - 4171 - 17
412GLYGLYVALVAL(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4101 - 10
422ASPASPASPASP(chain H and (resseq 401:410 or (resid 411 and (name...HH41111
432GLYGLYNH2NH2(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4171 - 17
442GLYGLYNH2NH2(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4171 - 17
452GLYGLYNH2NH2(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4171 - 17
462GLYGLYNH2NH2(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4171 - 17
472GLYGLYNH2NH2(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4171 - 17
482GLYGLYNH2NH2(chain H and (resseq 401:410 or (resid 411 and (name...HH401 - 4171 - 17
512GLYGLYVALVAL(chain J and (resseq 401:410 or (resid 411 and (name...JJ401 - 4101 - 10
522ASPASPASPASP(chain J and (resseq 401:410 or (resid 411 and (name...JJ41111
532GLYGLYNH2NH2(chain J and (resseq 401:410 or (resid 411 and (name...JJ401 - 4171 - 17
542GLYGLYNH2NH2(chain J and (resseq 401:410 or (resid 411 and (name...JJ401 - 4171 - 17
552GLYGLYNH2NH2(chain J and (resseq 401:410 or (resid 411 and (name...JJ401 - 4171 - 17
562GLYGLYNH2NH2(chain J and (resseq 401:410 or (resid 411 and (name...JJ401 - 4171 - 17
572GLYGLYNH2NH2(chain J and (resseq 401:410 or (resid 411 and (name...JJ401 - 4171 - 17

NCS ensembles :
ID
1
2

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Components

#1: Protein
Soluble acetylcholine receptor / acetylcholine binding protein


Mass: 23535.307 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8
#2: Protein/peptide
Alpha-conotoxin LvIA / Alpha-CTx LvIA


Mass: 1641.893 Da / Num. of mol.: 5 / Mutation: N29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus lividus (invertebrata) / Production host: Synthesium tursionis (invertebrata) / References: UniProt: L8BU87
Has ligand of interestY

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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: 4.87 Å3/Da / Density % sol: 74.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 50297 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 55.63 Å2 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.079 / Rrim(I) all: 0.277 / Χ2: 0.98 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.0713.21.75232770.7470.5041.8250.70399.8
3.07-3.1513.31.31432990.8350.3771.3690.69799.9
3.15-3.2313.31.43633030.8850.4131.4960.76799.9
3.23-3.3312.90.97132790.8720.2861.0131.098100
3.33-3.4312.81.64733320.9520.5021.7251.0799.9
3.43-3.5612.10.63732950.9740.2050.6711.06199.9
3.56-3.711.70.49533370.9660.1630.5231.16999.8
3.7-3.8713.30.80632960.9730.2320.8391.01799.8
3.87-4.0711.90.27733590.9790.0940.2930.99299.9
4.07-4.33140.1733270.9950.0470.1771.048100
4.33-4.6614.10.1433570.9960.0390.1460.986100
4.66-5.1314.20.11733730.9970.0320.1211.091100
5.13-5.8714.10.11133970.9980.0310.1150.974100
5.87-7.3913.80.08934490.9980.0250.0921.063100
7.39-5013.50.04636170.9990.0130.0480.9899.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO5

5co5


Resolution: 2.998→48.584 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.49
RfactorNum. reflection% reflection
Rfree0.3162 2410 5.05 %
Rwork0.2625 --
obs0.2652 47700 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.06 Å2 / Biso mean: 59.8322 Å2 / Biso min: 24.99 Å2
Refinement stepCycle: final / Resolution: 2.998→48.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8820 0 0 0 8820
Num. residues----1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139055
X-RAY DIFFRACTIONf_angle_d1.53312365
X-RAY DIFFRACTIONf_chiral_restr0.0761380
X-RAY DIFFRACTIONf_plane_restr0.0111600
X-RAY DIFFRACTIONf_dihedral_angle_d19.0575485
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4270X-RAY DIFFRACTION18.551TORSIONAL
12B4270X-RAY DIFFRACTION18.551TORSIONAL
13D4270X-RAY DIFFRACTION18.551TORSIONAL
14G4270X-RAY DIFFRACTION18.551TORSIONAL
15I4270X-RAY DIFFRACTION18.551TORSIONAL
21E361X-RAY DIFFRACTION18.551TORSIONAL
22C361X-RAY DIFFRACTION18.551TORSIONAL
23F361X-RAY DIFFRACTION18.551TORSIONAL
24H361X-RAY DIFFRACTION18.551TORSIONAL
25J361X-RAY DIFFRACTION18.551TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.998-3.05870.38311390.3076267397
3.0587-3.12520.33351340.27352763100
3.1252-3.19790.36971480.27442786100
3.1979-3.27780.38111240.3187276699
3.2778-3.36640.38211510.3272275099
3.3664-3.46550.59621170.4786229782
3.4655-3.57730.43221330.3995246688
3.5773-3.70510.54431340.4782227282
3.7051-3.85340.54871230.3924230983
3.8534-4.02870.43251150.359224781
4.0287-4.2410.24941640.2054278799
4.241-4.50650.23371510.1768278499
4.5065-4.85420.1851520.1628278899
4.8542-5.34210.22021500.1622839100
5.3421-6.11380.23821570.18362849100
6.1138-7.69790.21351540.20452893100
7.6979-48.5840.23151640.20123021100
Refinement TLS params.Method: refined / Origin x: -64.6842 Å / Origin y: 24.2529 Å / Origin z: -17.6663 Å
111213212223313233
T0.3003 Å20.0547 Å20.0223 Å2-0.3155 Å20.0052 Å2--0.3522 Å2
L0.519 °20.1629 °20.0141 °2-0.6152 °2-0.0591 °2--0.5943 °2
S-0.0206 Å °-0.085 Å °-0.0591 Å °-0.0684 Å °-0.0555 Å °-0.0894 Å °0.1084 Å °0.048 Å °0.0648 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 206
2X-RAY DIFFRACTION1allF401 - 417
3X-RAY DIFFRACTION1allB0 - 206
4X-RAY DIFFRACTION1allC401 - 417
5X-RAY DIFFRACTION1allD0 - 206
6X-RAY DIFFRACTION1allE401 - 417
7X-RAY DIFFRACTION1allG0 - 206
8X-RAY DIFFRACTION1allH401 - 417
9X-RAY DIFFRACTION1allI0 - 206
10X-RAY DIFFRACTION1allJ401 - 417

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