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- PDB-3hhg: Structure of CrgA, a LysR-type transcriptional regulator from Nei... -

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Basic information

Entry
Database: PDB / ID: 3hhg
TitleStructure of CrgA, a LysR-type transcriptional regulator from Neisseria meningitidis.
ComponentsTranscriptional regulator, LysR familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / Neisseria meningitidis / transcription factor / LysR / Structural Genomics / Oxford Protein Production Facility / OPPF / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function
: / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 ...: / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator CrgA
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSainsbury, S. / Ren, J. / Owens, R.J. / Stuart, D.I. / Oxford Protein Production Facility (OPPF)
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators
Authors: Sainsbury, S. / Lane, L.A. / Ren, J. / Gilbert, R.J. / Saunders, N.J. / Robinson, C.V. / Stuart, D.I. / Owens, R.J.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family
C: Transcriptional regulator, LysR family
D: Transcriptional regulator, LysR family
E: Transcriptional regulator, LysR family
F: Transcriptional regulator, LysR family
G: Transcriptional regulator, LysR family
H: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)272,2228
Polymers272,2228
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20460 Å2
ΔGint-141 kcal/mol
Surface area109380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.638, 119.091, 250.204
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
11A
21D
31B
41E
51G
61H
71C
81F
12A
22B
32C
42D
52E
62F
72G
82H
13A
23B
33C
43D
53E
63F
73G
83H
14A
24B
34C
44D
54E
64F
74G
84H

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLYSLYSAA2 - 442 - 44
211LYSLYSLYSLYSDD2 - 442 - 44
311LYSLYSLYSLYSBB2 - 442 - 44
411LYSLYSLYSLYSEE2 - 442 - 44
511LYSLYSLYSLYSGG2 - 442 - 44
611LYSLYSLYSLYSHH2 - 442 - 44
711LYSLYSLYSLYSCC2 - 442 - 44
811LYSLYSLYSLYSFF2 - 442 - 44
112GLNGLNASPASPAA92 - 15092 - 150
212GLNGLNASPASPBB92 - 15092 - 150
312GLNGLNASPASPCC92 - 15092 - 150
412GLNGLNASPASPDD92 - 15092 - 150
512GLNGLNASPASPEE92 - 15092 - 150
612GLNGLNASPASPFF92 - 15092 - 150
712GLNGLNASPASPGG92 - 15092 - 150
812GLNGLNASPASPHH92 - 15092 - 150
122PHEPHEGLUGLUAA268 - 292268 - 292
222PHEPHEGLUGLUBB268 - 292268 - 292
322PHEPHEGLUGLUCC268 - 292268 - 292
422PHEPHEGLUGLUDD268 - 292268 - 292
522PHEPHEGLUGLUEE268 - 292268 - 292
622PHEPHEGLUGLUFF268 - 292268 - 292
722PHEPHEGLUGLUGG268 - 292268 - 292
822PHEPHEGLUGLUHH268 - 292268 - 292
113ARGARGGLYGLYAA163 - 192163 - 192
213ARGARGGLYGLYBB163 - 192163 - 192
313ARGARGGLYGLYCC163 - 192163 - 192
413ARGARGGLYGLYDD163 - 192163 - 192
513ARGARGGLYGLYEE163 - 192163 - 192
613ARGARGGLYGLYFF163 - 192163 - 192
713ARGARGGLYGLYGG163 - 192163 - 192
813ARGARGGLYGLYHH163 - 192163 - 192
123ASNASNPROPROAA200 - 267200 - 267
223ASNASNPROPROBB200 - 267200 - 267
323ASNASNPROPROCC200 - 267200 - 267
423ASNASNPROPRODD200 - 267200 - 267
523ASNASNPROPROEE200 - 267200 - 267
623ASNASNPROPROFF200 - 267200 - 267
723ASNASNPROPROGG200 - 267200 - 267
823ASNASNPROPROHH200 - 267200 - 267
114GLNGLNALAALAAA65 - 8665 - 86
214GLNGLNALAALABB65 - 8665 - 86
314GLNGLNALAALACC65 - 8665 - 86
414GLNGLNALAALADD65 - 8665 - 86
514GLNGLNALAALAEE65 - 8665 - 86
614GLNGLNALAALAFF65 - 8665 - 86
714GLNGLNALAALAGG65 - 8665 - 86
814GLNGLNALAALAHH65 - 8665 - 86

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Transcriptional regulator, LysR family / Transcriptional regulation


Mass: 34027.719 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: CrgA, NMB1856 / Plasmid: OPPF3350 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JXW7

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% v/v MPD, 0.1M sodium acetate pH5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 43934 / % possible obs: 83.8 % / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.66 / % possible all: 85.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0047refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHF
Resolution: 3.2→29.88 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 46.634 / SU ML: 0.34 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.656 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28584 2165 5.1 %RANDOM
Rwork0.21426 ---
obs0.21787 40596 86.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.603 Å2
Baniso -1Baniso -2Baniso -3
1--4.2 Å20 Å20 Å2
2--0.26 Å20 Å2
3---3.94 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18304 0 0 0 18304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02218616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212631
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.97325203
X-RAY DIFFRACTIONr_angle_other_deg0.789330782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73352346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27323.817854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07153249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.97615152
X-RAY DIFFRACTIONr_chiral_restr0.0510.22915
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02120766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023738
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_it2.379411714
X-RAY DIFFRACTIONr_mcbond_other0.57944748
X-RAY DIFFRACTIONr_mcangle_it4.321618816
X-RAY DIFFRACTIONr_scbond_it4.10566902
X-RAY DIFFRACTIONr_scangle_it6.88106387
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
11A256medium positional0.315
11B256medium positional0.495
11C256medium positional0.35
11D256medium positional0.435
11E256medium positional0.355
11F256medium positional0.365
11G256medium positional0.35
11H256medium positional0.315
22A498medium positional0.335
22B498medium positional0.315
22C498medium positional0.425
22D498medium positional0.325
22E498medium positional0.35
22F498medium positional0.315
22G498medium positional0.485
22H498medium positional0.365
33A574medium positional0.285
33B574medium positional0.275
33C574medium positional0.315
33D574medium positional0.295
33E574medium positional0.285
33F574medium positional0.295
33G574medium positional0.395
33H574medium positional0.375
44A132medium positional0.35
44B132medium positional0.245
44C132medium positional0.285
44D132medium positional0.355
44E132medium positional0.385
44F132medium positional0.265
44G132medium positional0.35
44H132medium positional0.35
11A304loose positional1.1710
11B304loose positional1.2310
11C304loose positional0.8910
11D304loose positional1.2510
11E304loose positional1.2710
11F304loose positional1.510
11G304loose positional0.7810
11H304loose positional1.1210
22A639loose positional0.9910
22B639loose positional0.9310
22C639loose positional1.0410
22D639loose positional1.1410
22E639loose positional1.0210
22F639loose positional0.9310
22G639loose positional1.5510
22H639loose positional1.1210
33A668loose positional0.8810
33B668loose positional0.910
33C668loose positional110
33D668loose positional0.9510
33E668loose positional0.9510
33F668loose positional0.8910
33G668loose positional1.310
33H668loose positional1.2110
44A182loose positional1.2510
44B182loose positional1.0610
44C182loose positional1.4410
44D182loose positional1.7610
44E182loose positional1.0610
44F182loose positional1.1610
44G182loose positional1.5810
44H182loose positional1.6210
11A256medium thermal2.4215
11B256medium thermal2.9915
11C256medium thermal3.4315
11D256medium thermal4.0815
11E256medium thermal3.215
11F256medium thermal2.2115
11G256medium thermal2.7115
11H256medium thermal2.6615
22A498medium thermal5.4715
22B498medium thermal4.6815
22C498medium thermal4.815
22D498medium thermal3.2915
22E498medium thermal3.5715
22F498medium thermal3.2115
22G498medium thermal4.1315
22H498medium thermal4.2515
33A574medium thermal5.1415
33B574medium thermal5.9515
33C574medium thermal4.2415
33D574medium thermal4.3115
33E574medium thermal5.2115
33F574medium thermal3.3715
33G574medium thermal4.2415
33H574medium thermal4.7215
44A132medium thermal4.9815
44B132medium thermal7.0915
44C132medium thermal2.3915
44D132medium thermal4.5715
44E132medium thermal3.4415
44F132medium thermal3.4915
44G132medium thermal5.1515
44H132medium thermal4.315
11A304loose thermal3.1220
11B304loose thermal3.220
11C304loose thermal3.8420
11D304loose thermal3.7220
11E304loose thermal3.8220
11F304loose thermal2.320
11G304loose thermal2.9520
11H304loose thermal3.9520
22A639loose thermal5.6120
22B639loose thermal4.5320
22C639loose thermal5.0920
22D639loose thermal4.0420
22E639loose thermal3.9120
22F639loose thermal4.0920
22G639loose thermal3.9320
22H639loose thermal3.8720
33A668loose thermal5.120
33B668loose thermal5.5420
33C668loose thermal4.6920
33D668loose thermal4.5320
33E668loose thermal5.120
33F668loose thermal3.5920
33G668loose thermal4.0820
33H668loose thermal4.1720
44A182loose thermal4.3920
44B182loose thermal6.6120
44C182loose thermal4.1120
44D182loose thermal4.5720
44E182loose thermal3.5120
44F182loose thermal3.5520
44G182loose thermal4.1120
44H182loose thermal3.820
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 168 -
Rwork0.342 2969 -
obs--83.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.7462-0.8869-4.27269.0610.42624.46450.8469-1.12481.77661.0913-0.315-0.3463-0.5231.26-0.53190.5919-0.3729-0.20640.47490.11371.193735.71106.926181.279
28.50274.40651.62629.86510.68143.0987-0.27330.2786-0.81490.81790.20860.2457-0.0411-0.38550.06470.1431-0.02820.09680.1185-0.02830.178617.5649.242173.781
38.7431-1.59781.015810.0228-8.66147.922-0.01030.186-1.1606-0.7937-0.2187-0.47680.98680.26240.2290.31240.0544-0.02710.0307-0.09070.490840.36412.62101.905
49.07892.24062.78267.63050.80015.301-0.06170.16340.8342-0.601-0.09530.4025-0.7199-0.1560.1570.1570.0416-0.01120.0150.01850.134616.884106.861102.418
57.0907-0.98541.26117.7623-2.61629.60340.11881.5620.62060.06890.6308-0.4589-0.98530.9513-0.74960.1161-0.06850.13820.54950.03020.433445.045102.2390.889
63.2189-3.25393.7344.462-1.629.3840.58410.7885-0.6151-0.5937-0.67371.18840.7410.44270.08960.2624-0.0749-0.03760.8399-0.04270.499512.13220.12291.059
79.50741.9626-0.59375.1233-0.04675.29870.0755-0.5779-0.110.3959-0.017-0.33690.15510.4161-0.05850.16160.0001-0.11930.09580.00750.089243.72719.405186.407
88.67162.89421.11119.517-4.50295.94430.0357-1.166-0.321.82140.06461.09420.0121-0.5609-0.10030.74790.01080.44460.28510.15470.37539.22290.941183.645
920.7389-1.05165.77491.19660.98483.3153-0.01770.72940.25470.2138-0.0996-0.05790.24290.12610.11730.1675-0.0154-0.03450.06570.04590.081223.97698.18170.665
1030.494-0.9668-4.32590.392-0.13723.3929-0.01340.18630.45780.06650.0524-0.1274-0.1918-0.0668-0.0390.2025-0.0033-0.05540.0163-0.01320.085331.65919.924169.662
1126.54170.3111-5.19160.8173-1.16672.55950.0816-0.2141.01080.0315-0.0427-0.0691-0.04990.1322-0.0390.10660.01440.00180.08140.00940.113525.49722.483105.634
1225.20910.55116.13160.45870.38451.86920.41060.0254-1.18270.1752-0.1238-0.0160.21320.0542-0.28680.0703-0.036-0.01440.0938-0.0140.113231.73496.928105.888
1326.21723.99085.72361.39410.81371.60740.2724-0.0402-0.3284-0.1069-0.2078-0.07630.155-0.0736-0.06470.0680.05210.030.15810.03270.083330.14892.39896.428
1436.39524.1511-10.42671.6619-1.26224.44540.08450.55170.738-0.31520.15380.19740.058-0.1866-0.23830.1343-0.0025-0.04180.08930.05280.108227.10927.58496.714
1515.4231-2.5139-1.00131.6681.46461.43040.0590.47360.3348-0.1144-0.002-0.0743-0.17170.0262-0.0570.3158-0.0088-0.04370.14170.05160.095929.06225.699177.942
1618.6941-4.04325.59832.1241-0.70741.89810.05480.6008-0.5931-0.04190.10880.09560.00710.3344-0.16360.2259-0.0057-0.03020.25410.0430.104126.30289.687176.305
176.0297-2.2672-2.35824.8156-0.17722.0338-0.2356-0.3518-0.22940.30160.1438-0.28990.08720.30240.09180.02790.0307-0.04580.1106-0.07190.272532.84997.486148.612
185.1343-1.45941.79674.62660.11951.4508-0.1736-0.5371-0.0540.25160.27170.1516-0.2063-0.2951-0.09810.06060.04120.04150.28230.17130.285124.34521.011148.203
197.91561.2244.041.45761.01822.90470.05930.0605-0.4454-0.20030.14350.0271-0.14290.1674-0.20280.0543-0.02240.01550.07890.13740.365834.68920.58127.975
207.09230.577-2.65252.8399-1.30581.9189-0.11950.21020.1849-0.30820.1337-0.11340.1183-0.1186-0.01410.0401-0.0047-0.01520.0665-0.11810.263722.51398.288128.398
215.4092-3.2411.02954.65940.52881.1701-0.04560.16540.3460.1378-0.1031-0.18620.0167-0.04990.14870.0164-0.04210.00570.22610.04710.367936.17168.70793.452
224.9333-2.2659-0.73833.923-0.85241.3413-0.1565-0.2412-0.31090.30730.080.42340.06170.02540.07650.0592-0.03960.04470.1885-0.00170.39721.30850.67993.423
233.68630.3617-0.41023.49890.06911.9827-0.06360.1641-0.2149-0.2182-0.236-0.44030.33730.28660.29960.8140.2752-0.03460.7026-0.0130.949834.80548.244178.685
244.0730.32650.76383.77410.31592.9472-0.15650.333-0.1011-0.3355-0.08120.59560.0301-0.2090.23770.62490.1638-0.0540.47330.08440.64220.83566.307177.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 62
2X-RAY DIFFRACTION2F2 - 62
3X-RAY DIFFRACTION3E2 - 62
4X-RAY DIFFRACTION4B2 - 62
5X-RAY DIFFRACTION5C2 - 62
6X-RAY DIFFRACTION6D2 - 62
7X-RAY DIFFRACTION7G2 - 62
8X-RAY DIFFRACTION8H2 - 62
9X-RAY DIFFRACTION9A63 - 89
10X-RAY DIFFRACTION10F63 - 89
11X-RAY DIFFRACTION11E63 - 89
12X-RAY DIFFRACTION12B63 - 89
13X-RAY DIFFRACTION13C63 - 89
14X-RAY DIFFRACTION14D63 - 89
15X-RAY DIFFRACTION15G63 - 89
16X-RAY DIFFRACTION16H63 - 89
17X-RAY DIFFRACTION17A90 - 292
18X-RAY DIFFRACTION18F90 - 292
19X-RAY DIFFRACTION19E90 - 292
20X-RAY DIFFRACTION20B90 - 292
21X-RAY DIFFRACTION21C90 - 292
22X-RAY DIFFRACTION22D90 - 292
23X-RAY DIFFRACTION23G90 - 292
24X-RAY DIFFRACTION24H90 - 292

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