6YU9
CO-dehydrogenase homodimer from Clostridium autoethanogenum at 1.90-A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6YTT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 291.15 | Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96-well MRC 2 Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 uL of mother liquor, crystallization drop contained a mixture of 0.6 uL protein and 0.6 uL precipitant. The protein concentration was 16.9 mg/mL in 25 mM Tris/HCl pH7.6, 10% glycerol (v/v) and 2 mM dithiothreitol. The best diffracting crystal of CODH was obtained by initial screening using the Shotgun (SG1) screen from Molecular dimensions. The crystallization reservoir contained 200 mM Magnesium acetate tetrahydrate; 20% (w/v) polyethylene glycol 3350. Crystals were cryo protected in the same solution supplemented with 25% glycerol (v/v). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 52.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.531 | α = 90 |
b = 109.446 | β = 112.55 |
c = 129.28 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS PILATUS 2M-F | 2019-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00004 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.9 | 119.4 | 93.3 | 0.205 | 0.223 | 0.088 | 0.993 | 7.7 | 6.2 | 102786 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 2.179 | 63.9 | 0.804 | 0.928 | 0.45 | 0.611 | 1.8 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6YTT | 1.904 | 49.75 | 102786 | 5293 | 48 | 0.1598 | 0.1575 | 0.2026 | RANDOM | 33.12 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.5935 | 2.0385 | 2.2535 | -3.847 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.32 |
t_omega_torsion | 3.58 |
t_angle_deg | 1.12 |
t_bond_d | 0.011 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 18851 |
Nucleic Acid Atoms | |
Solvent Atoms | 1107 |
Heterogen Atoms | 113 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
STARANISO | data scaling |
MOLREP | phasing |