2OMK
Structure of the Bacteroides Thetaiotaomicron Thiamin Pyrophosphokinase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.7 | 295 | 0.05 M Potassium phosphate monobasic, 20 % w/v Polyethylene glycol 8000, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 39.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.309 | α = 90 |
b = 66.084 | β = 99.9 |
c = 57.552 | 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 | CCD | MARRESEARCH | Mirrors | 2006-04-17 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MARRESEARCH | Mirrors | 2006-12-17 | M | SINGLE WAVELENGTH | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 1.0000 | APS | 5ID-B |
2 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.9787 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.8 | 45 | 94.8 | 0.071 | 23.7 | 6.9 | 36873 | 36873 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2 | 1.8 | 1.86 | 67.1 | 0.3 | 5.5 | 4.5 | 2577 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.8 | 30 | 34895 | 1829 | 95.02 | 0.1664 | 0.16454 | 0.20025 | RANDOM | 20.827 |
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] | |
0.81 | 0.46 | -0.66 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.908 |
r_dihedral_angle_4_deg | 15.551 |
r_dihedral_angle_3_deg | 13.641 |
r_dihedral_angle_1_deg | 5.964 |
r_scangle_it | 3.096 |
r_scbond_it | 2.027 |
r_mcangle_it | 1.341 |
r_angle_refined_deg | 1.094 |
r_mcbond_it | 0.815 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3344 |
Nucleic Acid Atoms | |
Solvent Atoms | 490 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |
SHELX | phasing |
SHARP | phasing |