5COJ
Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with native substrate 2-(4-methyl-1,3-thiazol-5-yl)ethanol.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293.2 | 18 - 22 % PEG 3,350 (w/v), 0.2 M magnesium formate, 5 % isopropanol (v/v), soaked with 0.5 mM 2-(4-methyl-1,3-thiazol-5-yl)ethanol | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.33 | 47.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 62.549 | α = 92.18 |
| b = 62.741 | β = 91.44 |
| c = 108.459 | γ = 101.32 |
| Symmetry | |
|---|---|
| Space Group | P 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 | MAR CCD 165 mm | 2012-01-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.81 | EMBL/DESY, HAMBURG | X13 |
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 | 1.9 | 20 | 94.7 | 0.027 | 21.8 | 2 | 119565 | ||||||||||||
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 | THROUGHOUT | 1.9 | 20 | 117078 | 6189 | 97.59 | 0.18729 | 0.18615 | 0.20951 | RANDOM | 37.845 | ||||||||
| 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] | |
| 0.77 | -0.23 | -1.79 | -1.97 | -2.1 | 1.77 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.035 |
| r_dihedral_angle_4_deg | 20.371 |
| r_dihedral_angle_3_deg | 13.555 |
| r_dihedral_angle_1_deg | 6.565 |
| r_long_range_B_refined | 5.212 |
| r_long_range_B_other | 5.184 |
| r_scangle_other | 2.655 |
| r_mcangle_it | 2.061 |
| r_mcangle_other | 2.05 |
| r_scbond_it | 1.741 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11149 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 371 |
| Heterogen Atoms | 58 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
