5X8D
D90L mutant of thermus thermophilus HB8 thymidylate kinase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICROBATCH | 295 | 0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.1 | 36.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.8 | α = 90 |
| b = 47.32 | β = 90 |
| c = 153.04 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2016-10-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.54178 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.26 | 76.64 | 91.9 | 9.3 | 7.9 | 15291 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 2.26 | 2.33 | |||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5X7J | 2.26 | 76.64 | 15242 | 721 | 91.55 | 0.2203 | 0.2181 | 0.2629 | RANDOM | 21.8676 | ||||||
| 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] | |
| -0.43 | -0.3 | 0.72 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.874 |
| r_dihedral_angle_4_deg | 19.562 |
| r_dihedral_angle_3_deg | 16.15 |
| r_dihedral_angle_1_deg | 5.286 |
| r_angle_other_deg | 3.616 |
| r_mcangle_it | 1.678 |
| r_angle_refined_deg | 1.292 |
| r_mcbond_it | 0.913 |
| r_mcbond_other | 0.912 |
| r_chiral_restr | 0.064 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2844 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 82 |
| Heterogen Atoms | 25 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PDB_EXTRACT | data extraction |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
