8BQH
W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1.5 min
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6SDR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.361 | α = 90 |
b = 127.456 | β = 90 |
c = 128.952 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER2 S 16M | 2022-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.8856 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.61 | 90.65 | 94.14 | 0.996 | 9.5 | 5.7 | 94816 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.61 | 1.78 | 0.6555 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6SDR | 1.61 | 90.65 | 94816 | 4778 | 68.517 | 0.152 | 0.1509 | 0.1754 | 19.364 |
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] | |
0.132 | -0.062 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.373 |
r_dihedral_angle_4_deg | 19.159 |
r_dihedral_angle_3_deg | 13.409 |
r_lrange_it | 7.282 |
r_lrange_other | 7.264 |
r_dihedral_angle_1_deg | 6.894 |
r_scangle_it | 6.18 |
r_scangle_other | 6.18 |
r_scbond_other | 4.572 |
r_scbond_it | 4.56 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9126 |
Nucleic Acid Atoms | |
Solvent Atoms | 557 |
Heterogen Atoms | 230 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data processing |
STARANISO | data scaling |
PHASER | phasing |
autoPROC | data reduction |