8CM7
W-formate dehydrogenase M405A from Desulfovibrio vulgaris
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6SDR |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 30% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.31 | 46.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.874 | α = 90 |
b = 123.833 | β = 90 |
c = 149.891 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER X 4M | 2022-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.117 | 75.058 | 92.3 | 0.994 | 8.31 | 6.9 | 47566 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.117 | 2.298 | 0.613 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6SDR | 2.117 | 75.058 | 47565 | 2417 | 68.356 | 0.2 | 0.197 | 0.2518 | 38.585 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-0.448 | 0.016 | 0.433 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.371 |
r_dihedral_angle_4_deg | 17.924 |
r_dihedral_angle_3_deg | 15.223 |
r_dihedral_angle_1_deg | 7.583 |
r_lrange_it | 6.417 |
r_lrange_other | 6.409 |
r_scangle_it | 4.47 |
r_scangle_other | 4.47 |
r_mcangle_it | 4.239 |
r_mcangle_other | 4.239 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9149 |
Nucleic Acid Atoms | |
Solvent Atoms | 167 |
Heterogen Atoms | 185 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
autoPROC | data processing |
STARANISO | data scaling |
PHASER | phasing |
XDS | data reduction |
Aimless | data scaling |
XSCALE | data scaling |
pointless | data scaling |