6YUA
CO-dehydrogenase coupled to the N-terminal domain of the Acetyl-CoA synthase from Clostridium autoethanogenum isolated after tryptic digestion.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6YTT |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
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 28.5 mg/mL in 25 mM Tris pH 7.6, 10% (v/v) glycerol and 2 mM dithiothreitol. The best diffracting crystal of CODH bound to the ACS N-terminal domain was obtained by initial screening using the Shotgun (SG1) screen from Molecular dimensions. The crystallization reservoir contained 200 mM Magnesium chloride hexahydrate and 20% (w/v) polyethylene glycol 3350. The crystal was cryoprotected in the same crystallization solution supplemented with 25% ethylene glycol. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.61 | 52.98 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 89.333 | α = 90 |
b = 89.333 | β = 90 |
c = 527.13 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 41 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2019-12-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00000 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.14 | 131.783 | 84.3 | 0.26 | 0.268 | 0.061 | 0.999 | 8.9 | 17.7 | 17564 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.14 | 3.576 | 81.2 | 1.492 | 1.524 | 0.309 | 0.748 | 2.5 | 23.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6YTT | 3.16 | 39.95 | 1.35 | 17526 | 893 | 45.91 | 0.2252 | 0.2238 | 0.252 | 65.4363 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 13810 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 62 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
STARANISO | data scaling |
MOLREP | phasing |