3BHD
Crystal structure of human thiamine triphosphatase (THTPA)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 3.8 | 300 | 50mM Citric acid, 0.2M Ammonium sulfate, 3mM Sodium tungstenate, 10mg/ml Protein, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.793 | 31.396 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 60.77 | α = 90 |
| b = 46.81 | β = 113.97 |
| c = 71.87 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2007-09-13 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.97915 | ESRF | ID14-2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.5 | 20 | 99.6 | 0.061 | 13.79 | 3.51 | 115663 | -3 | 20.28 | ||||||||||
| 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 | 1.5 | 1.6 | 99.7 | 0.421 | 3.1 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1.5 | 19.96 | 59035 | 59035 | 2983 | 99.5 | 0.17774 | 0.17648 | 0.20117 | RANDOM | 15.948 | ||||||
| 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] | |
| -0.01 | -0.01 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.093 |
| r_dihedral_angle_4_deg | 20.614 |
| r_dihedral_angle_3_deg | 13.269 |
| r_dihedral_angle_1_deg | 6.567 |
| r_scangle_it | 4.217 |
| r_scbond_it | 2.691 |
| r_mcangle_it | 1.639 |
| r_angle_refined_deg | 1.605 |
| r_mcbond_it | 0.94 |
| r_metal_ion_refined | 0.884 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3261 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 225 |
| Heterogen Atoms | 77 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XSCALE | data scaling |
| SHELX | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ProDC | data collection |
| SHELXD | phasing |
