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- PDB-3mk7: The structure of CBB3 cytochrome oxidase -

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Basic information

Entry
Database: PDB / ID: 3mk7
TitleThe structure of CBB3 cytochrome oxidase
Components
  • (Cytochrome c oxidase, cbb3-type, subunit ...) x 3
  • 30-mer peptide
KeywordsOXIDOREDUCTASE / TM helices
Function / homology
Function and homology information


aerobic respiration, using ferrous ions as electron donor / : / : / cytochrome complex / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity ...aerobic respiration, using ferrous ions as electron donor / : / : / cytochrome complex / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / : / proton transmembrane transport / oxygen binding / electron transfer activity / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2250 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #130 / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome C Oxidase; Chain A ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2250 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #130 / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Helix non-globular / Special / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEXACYANOFERRATE(3-) / HEME C / PROTOPORPHYRIN IX CONTAINING FE / HYDROGEN PEROXIDE / PHOSPHATE ION / Cbb3-type cytochrome c oxidase subunit CcoN1 / Cbb3-type cytochrome c oxidase subunit II / Cbb3-type cytochrome c oxidase subunit CcoP1
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsBuschmann, S. / Warkentin, E. / Michel, H. / Ermler, U.
CitationJournal: Science / Year: 2010
Title: The Structure of cbb3 Cytochrome Oxidase Provides Insights into Proton Pumping
Authors: Buschmann, S. / Warkentin, E. / Xie, H. / Langer, J.D. / Ermler, U. / Michel, H.
History
DepositionApr 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase, cbb3-type, subunit N
B: Cytochrome c oxidase, cbb3-type, subunit O
C: Cytochrome c oxidase, cbb3-type, subunit P
D: Cytochrome c oxidase, cbb3-type, subunit N
E: Cytochrome c oxidase, cbb3-type, subunit O
F: Cytochrome c oxidase, cbb3-type, subunit P
G: Cytochrome c oxidase, cbb3-type, subunit N
H: Cytochrome c oxidase, cbb3-type, subunit O
I: Cytochrome c oxidase, cbb3-type, subunit P
K: Cytochrome c oxidase, cbb3-type, subunit N
L: Cytochrome c oxidase, cbb3-type, subunit O
M: Cytochrome c oxidase, cbb3-type, subunit P
U: 30-mer peptide
X: 30-mer peptide
Y: 30-mer peptide
Z: 30-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,02860
Polymers447,73616
Non-polymers14,29244
Water00
1
A: Cytochrome c oxidase, cbb3-type, subunit N
B: Cytochrome c oxidase, cbb3-type, subunit O
C: Cytochrome c oxidase, cbb3-type, subunit P
U: 30-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50715
Polymers111,9344
Non-polymers3,57311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15980 Å2
ΔGint-127 kcal/mol
Surface area36030 Å2
MethodPISA
2
D: Cytochrome c oxidase, cbb3-type, subunit N
E: Cytochrome c oxidase, cbb3-type, subunit O
F: Cytochrome c oxidase, cbb3-type, subunit P
X: 30-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50715
Polymers111,9344
Non-polymers3,57311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-126 kcal/mol
Surface area35660 Å2
MethodPISA
3
G: Cytochrome c oxidase, cbb3-type, subunit N
H: Cytochrome c oxidase, cbb3-type, subunit O
I: Cytochrome c oxidase, cbb3-type, subunit P
Y: 30-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50715
Polymers111,9344
Non-polymers3,57311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15990 Å2
ΔGint-127 kcal/mol
Surface area35850 Å2
MethodPISA
4
K: Cytochrome c oxidase, cbb3-type, subunit N
L: Cytochrome c oxidase, cbb3-type, subunit O
M: Cytochrome c oxidase, cbb3-type, subunit P
Z: 30-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50715
Polymers111,9344
Non-polymers3,57311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15950 Å2
ΔGint-126 kcal/mol
Surface area35990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.475, 279.933, 175.192
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
21D
31G
41K
12A
22D
32G
42K
13B
23E
33H
43L
14B
24E
34H
44L
15C
25F
35I
45M
16C
26F
36I
46M
17F
27I
37M

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A5 - 265
2111D5 - 265
3111G5 - 265
4111K5 - 265
1211A269 - 470
2211D269 - 470
3211G269 - 470
4211K269 - 470
1311A501 - 508
2311D501 - 508
3311G501 - 508
4311K501 - 508
1121A266 - 268
2121D266 - 268
3121G266 - 268
4121K266 - 268
1131B1 - 37
2131E1 - 37
3131H1 - 37
4131L1 - 37
1141B38 - 211
2141E38 - 211
3141H38 - 211
4141L38 - 211
1151C1 - 93
2151F1 - 93
3151I1 - 93
4151M1 - 93
1161C94 - 213
2161F94 - 213
3161I94 - 213
4161M94 - 213
1261C - M226 - 323
2261F - I226 - 323
3261I - F226 - 323
4261M - C226 - 323
1171F214 - 225
2171I214 - 225
3171M214 - 225

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Cytochrome c oxidase, cbb3-type, subunit ... , 3 types, 12 molecules ADGKBEHLCFIM

#1: Protein
Cytochrome c oxidase, cbb3-type, subunit N


Mass: 52829.637 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas stutzeri (bacteria) / Genus: ATCC 14405 / Strain: ZoBell / References: UniProt: D9IA43*PLUS
#2: Protein
Cytochrome c oxidase, cbb3-type, subunit O


Mass: 22842.102 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas stutzeri (bacteria) / Genus: ATCC 14405 / Strain: ZoBell / References: UniProt: D9IA44*PLUS
#3: Protein
Cytochrome c oxidase, cbb3-type, subunit P


Mass: 33691.051 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas stutzeri (bacteria) / Genus: ATCC 14405 / Strain: ZoBell / References: UniProt: D9IA45*PLUS

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Protein/peptide , 1 types, 4 molecules UXYZ

#4: Protein/peptide
30-mer peptide


Mass: 2571.161 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas stutzeri (bacteria) / Genus: ATCC 14405 / Strain: ZoBell

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Non-polymers , 7 types, 44 molecules

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


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O2
#9: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#10: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Chemical
ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6FeN6

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Details

Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR ALL CHAINS DO NOT CURRENTLY EXIST. THE AUTHORS COULD NOT ...THE SEQUENCE DATABASE REFERENCES FOR ALL CHAINS DO NOT CURRENTLY EXIST. THE AUTHORS COULD NOT IDENTIFY THE CORRESPONDING GENE OF CHAIN U, X, Y, Z.

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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: 3.74 Å3/Da / Density % sol: 67.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM Tris(HCl), 0.1M NaCl, 0.058% alpha-UDM, 0.0125% decanoylsucrose, 0.018% alpha-DDM, 0.016M K3Fe(CN)6, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 3.2→150 Å / Num. all: 109170 / Num. obs: 109170 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.162 / Rsym value: 0.111 / Net I/σ(I): 11.4
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.4 / Num. unique all: 9703 / Rsym value: 0.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
SHARPphasing
REFMAC5.6.0046refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 38.557 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. RESOLUTION RANGE ACTUALLY USED 3.0 TO 15A, COMPLETENESS 98.76, REFLECTIONS 125112, R= 0.200, RFREE= 0.233, RESOLUTION 3.0 TO 3.075, ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. RESOLUTION RANGE ACTUALLY USED 3.0 TO 15A, COMPLETENESS 98.76, REFLECTIONS 125112, R= 0.200, RFREE= 0.233, RESOLUTION 3.0 TO 3.075, COMPLETENESS 99.8%, R=0.360, RFREE=0.367
RfactorNum. reflection% reflectionSelection details
Rfree0.22341 5480 5.1 %RANDOM
Rwork0.189 ---
obs0.19074 102875 98.52 %-
all-125112 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.308 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.58 Å20 Å2
3----4.63 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30738 0 952 0 31690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02232772
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3282.01644852
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64653963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17723.0841284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.222154755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.48415136
X-RAY DIFFRACTIONr_chiral_restr0.0930.24695
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125064
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
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
11A3732TIGHT POSITIONAL0.040.05
12D3732TIGHT POSITIONAL0.030.05
13G3732TIGHT POSITIONAL0.030.05
14K3732TIGHT POSITIONAL0.030.05
11A3732TIGHT THERMAL4.510.5
12D3732TIGHT THERMAL6.240.5
13G3732TIGHT THERMAL4.440.5
14K3732TIGHT THERMAL6.490.5
21A27TIGHT POSITIONAL0.030.05
22D27TIGHT POSITIONAL0.020.05
23G27TIGHT POSITIONAL0.020.05
24K27TIGHT POSITIONAL0.030.05
21A27TIGHT THERMAL3.680.5
22D27TIGHT THERMAL5.610.5
23G27TIGHT THERMAL3.730.5
24K27TIGHT THERMAL5.70.5
31B247TIGHT POSITIONAL0.030.05
32E247TIGHT POSITIONAL0.020.05
33H247TIGHT POSITIONAL0.020.05
34L247TIGHT POSITIONAL0.020.05
31B247TIGHT THERMAL8.120.5
32E247TIGHT THERMAL9.210.5
33H247TIGHT THERMAL6.160.5
34L247TIGHT THERMAL7.720.5
41B1344TIGHT POSITIONAL0.050.05
42E1344TIGHT POSITIONAL0.040.05
43H1344TIGHT POSITIONAL0.040.05
44L1344TIGHT POSITIONAL0.040.05
41B1344TIGHT THERMAL4.970.5
42E1344TIGHT THERMAL6.210.5
43H1344TIGHT THERMAL5.120.5
44L1344TIGHT THERMAL5.580.5
51C743TIGHT POSITIONAL0.030.05
52F743TIGHT POSITIONAL0.020.05
53I743TIGHT POSITIONAL0.030.05
54M743TIGHT POSITIONAL0.030.05
51C743TIGHT THERMAL80.5
52F743TIGHT THERMAL9.150.5
53I743TIGHT THERMAL8.470.5
54M743TIGHT THERMAL10.880.5
61C1589TIGHT POSITIONAL0.050.05
62F1589TIGHT POSITIONAL0.040.05
63I1589TIGHT POSITIONAL0.050.05
64M1589TIGHT POSITIONAL0.050.05
61C1589TIGHT THERMAL5.630.5
62F1589TIGHT THERMAL9.020.5
63I1589TIGHT THERMAL4.770.5
64M1589TIGHT THERMAL6.020.5
71F79TIGHT POSITIONAL0.050.05
72I79TIGHT POSITIONAL0.040.05
73M79TIGHT POSITIONAL0.050.05
71F79TIGHT THERMAL8.760.5
72I79TIGHT THERMAL5.430.5
73M79TIGHT THERMAL9.320.5
LS refinement shellResolution: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 396 -
Rwork0.282 7379 -
obs--99.96 %
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)
11.27710.02940.86890.95580.43893.7343-0.1358-0.2721-0.0330.36770.045-0.05120.10570.38570.09080.28740.14220.04850.23190.05030.229899.187111.634168.352
23.08972.9509-1.96069.4587-4.70244.621-0.5312-0.0011-1.22-0.27660.2451-0.30081.1096-0.3120.28620.77090.10310.17260.50750.05551.1249103.40351.251135.924
31.0650.0243-1.05031.0094-0.72325.1130.03020.5685-0.0597-0.3392-0.09730.1506-0.1707-0.46280.06710.49430.1426-0.05670.452-0.11750.278994.465104.59484.834
42.34750.8610.65822.91131.74132.8385-0.06450.1912-0.3534-0.0507-0.82041.44450.3892-1.36740.88490.3144-0.1066-0.00190.8405-0.56461.272739.265109.77128.156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 470
2X-RAY DIFFRACTION1A501 - 508
3X-RAY DIFFRACTION1U701 - 730
4X-RAY DIFFRACTION1B6 - 211
5X-RAY DIFFRACTION1C1 - 323
6X-RAY DIFFRACTION2D6 - 470
7X-RAY DIFFRACTION2D501 - 508
8X-RAY DIFFRACTION2X701 - 730
9X-RAY DIFFRACTION2E6 - 211
10X-RAY DIFFRACTION2F1 - 323
11X-RAY DIFFRACTION3G6 - 470
12X-RAY DIFFRACTION3G501 - 508
13X-RAY DIFFRACTION3Y701 - 730
14X-RAY DIFFRACTION3H6 - 211
15X-RAY DIFFRACTION3I1 - 323
16X-RAY DIFFRACTION4K6 - 470
17X-RAY DIFFRACTION4K501 - 508
18X-RAY DIFFRACTION4Z701 - 730
19X-RAY DIFFRACTION4L6 - 211
20X-RAY DIFFRACTION4M1 - 323

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