8QMF
Transketolase from Vibrio vulnificus in complex with thiamin pyrophosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.23 | α = 90 |
b = 75.48 | β = 99.87 |
c = 130.39 | 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 6M | 2022-04-15 | 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) | Rrim 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 | 2.1 | 34.95 | 99.39 | 0.087 | 0.997 | 11.66 | 3.19 | 76983 | 35.13 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.1 | 2.2 | 99.6 | 0.896 | 0.675 | 1.95 | 3.19 |
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 | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.1 | 34.95 | 1.35 | 76958 | 3849 | 99.39 | 0.1647 | 0.1625 | 0.207 | 37.59 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.9895 |
f_angle_d | 0.8229 |
f_chiral_restr | 0.0503 |
f_plane_restr | 0.0074 |
f_bond_d | 0.0066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10356 |
Nucleic Acid Atoms | |
Solvent Atoms | 715 |
Heterogen Atoms | 103 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |