4WQ9
Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - dithionite soak
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.28 | 293.15 | 23.5% (w/v) PEG 3350, 0.1 M Bis-tris pH 6.28, 0.2 M (NH4)2SO4, 0.1 M NaI |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.289 | α = 90 |
b = 69.864 | β = 129.42 |
c = 57.805 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100.15 | PIXEL | DECTRIS PILATUS 6M | 2013-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 1.2395 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.47 | 34.96 | 93 | 0.09 | 9.01 | 3.2 | 66925 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.47 | 1.52 | 86 | 0.53 | 1.93 | 2.7 | 5738 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.47 | 34.96 | 1.89 | 66843 | 3272 | 82.05 | 0.1421 | 0.1402 | 0.15 | 0.1785 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.262 |
f_angle_d | 1.524 |
f_chiral_restr | 0.073 |
f_bond_d | 0.018 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1727 |
Nucleic Acid Atoms | |
Solvent Atoms | 234 |
Heterogen Atoms | 103 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Coot | model building |
PHENIX | refinement |
XSCALE | data scaling |