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- PDB-2zt9: Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. P... -

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Basic information

Entry
Database: PDB / ID: 2zt9
TitleCrystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6
  • Cytochrome b6-f complex iron-sulfur subunit 1
KeywordsPHOTOSYNTHESIS / CYTOCHROME B6F COMPLEX / heme b / 2Fe-2S PROTEIN / CYTOCHROME F
Function / homology
Function and homology information


cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / : / photosynthesis / respiratory electron transport chain ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / : / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 ...Single helix bin / plastocyanin oxidoreductase / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rudiment single hybrid motif / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / Chem-SQD / Cytochrome b6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8 ...BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / Chem-SQD / Cytochrome b6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit 6 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit 1 / Cytochrome b6-f complex subunit 4
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCraner, W.A. / Baniulis, D. / Yamashita, E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120
Authors: Baniulis, D. / Yamashita, E. / Whitelegge, J.P. / Zatsman, A.I. / Hendrich, M.P. / Hasan, S.S. / Ryan, C.M. / Cramer, W.A.
History
DepositionSep 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Jun 20, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 2, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_validate_close_contact ...database_PDB_caveat / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 2.0Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 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: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit 1
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,20121
Polymers106,2428
Non-polymers7,95913
Water543
1
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit 1
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules

A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit 1
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,40342
Polymers212,48416
Non-polymers15,91926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area83480 Å2
ΔGint-908 kcal/mol
Surface area79200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.225, 159.225, 365.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein Cytochrome b6


Mass: 24291.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P0A384
#3: Protein Apocytochrome f / Cytochrome f


Mass: 31178.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: Q93SW9
#4: Protein Cytochrome b6-f complex iron-sulfur subunit 1 / Rieske iron-sulfur protein 1 / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein 1 ...Rieske iron-sulfur protein 1 / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein 1 / ISP 1 / RISP 1


Mass: 19216.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: Q93SX0, EC: 1.10.99.1

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Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17548.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: Q93SX1
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit VI / Cytochrome b6-f complex subunit petL


Mass: 3227.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: Q8YVQ2
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit VII / Cytochrome b6-f complex subunit petM


Mass: 3547.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P0A3Y1
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit V / Cytochrome b6-f complex subunit petG


Mass: 3997.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58246
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit VIII / Cytochrome b6-f complex subunit petN


Mass: 3234.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P61048

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Non-polymers , 8 types, 16 molecules

#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#11: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#12: Chemical ChemComp-OPC / (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE / DIOLEOYL-PHOSPHATIDYLCHOLINE


Mass: 801.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H87NO8P / Comment: phospholipid*YM
#13: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#15: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.029851 Å3/Da / Density % sol: 79.601486 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 54614 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+74 / Resolution: 3→45.69 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.51 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.442 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25908 2770 5.1 %RANDOM
Rwork0.22996 ---
obs0.23142 51833 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å20 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 3→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7364 0 545 3 7912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7922.07811121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90424.146287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.968151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7041526
X-RAY DIFFRACTIONr_chiral_restr0.130.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.23848
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2090.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5281.54843
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94627675
X-RAY DIFFRACTIONr_scbond_it0.98633937
X-RAY DIFFRACTIONr_scangle_it1.7174.53434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.004→3.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 200 -
Rwork0.307 3742 -
obs--98.87 %
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)
16.68690.78061.26765.00470.03322.53420.3595-0.59660.25740.7439-0.13670.7766-0.45-0.7421-0.2229-0.06570.04870.3155-0.0657-0.05650.1668-78.640272.946655.8835
21.7069-0.01011.68733.91921.78392.74140.3690.45610.0882-0.1283-0.01661.24490.1804-0.6362-0.3524-0.15410.13120.04730.0751-0.01360.2788-85.013469.752142.3489
31.62270.7867-0.78950.5512-0.20940.56120.09110.13440.65650.21660.13080.4628-0.2462-0.1236-0.2219-0.0011-0.02710.0109-0.06340.05690.1021-47.618193.881319.1706
40.00690.1636-0.04819.7748-2.00910.4627-0.1185-0.6278-1.0714-0.24660.2219-0.63540.43180.3988-0.10340.20040.2722-0.28170.3079-0.69520.553-69.494420.3974-19.3467
51.33950.29060.73441.95620.99571.0660.12340.3891-0.08130.0086-0.02910.15520.01030.0403-0.0943-0.17060.0625-0.07840.204-0.0945-0.0628-73.513557.0197-6.2724
64.42492.1915-0.47931.5260.11040.62330.08050.47860.3911-0.04970.02130.1182-0.19220.046-0.1019-0.0715-0.041-0.0008-0.00930.15650.0773-42.566694.20729.5018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D100 - 148
2X-RAY DIFFRACTION2D54 - 99
3X-RAY DIFFRACTION2D149 - 179
4X-RAY DIFFRACTION3D9 - 46
5X-RAY DIFFRACTION4C171 - 233
6X-RAY DIFFRACTION5C1 - 169
7X-RAY DIFFRACTION5C236 - 251
8X-RAY DIFFRACTION6C253 - 288

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