Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 2093)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 298 | 1.8-2.1 M AMMONIUM SULFATE, 0.2 M SODIUM CHLORIDE, 0.1 M SODIUM CACODYLATE, PH 6.2-6.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.95 | 68.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.64 | α = 90 |
| b = 106.23 | β = 90 |
| c = 208.28 | 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 | PIXEL | DECTRIS PILATUS 6M | 2016-06-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.98 | SSRL | BL9-2 |
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 | 2.7 | 104.14 | 100 | 0.2 | 6.8 | 6.6 | 54250 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.7 | 104.14 | 51494 | 2681 | 99.9 | 0.205 | 0.204 | 0.21 | 0.231 | 0.23 | RANDOM | 55.58 | |||||
| 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] | |
| 8.06 | -3.63 | -4.43 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.998 |
| r_dihedral_angle_4_deg | 14.902 |
| r_dihedral_angle_3_deg | 13.952 |
| r_long_range_B_refined | 7.967 |
| r_long_range_B_other | 7.967 |
| r_scangle_other | 6.197 |
| r_dihedral_angle_1_deg | 5.785 |
| r_mcangle_it | 4.738 |
| r_mcangle_other | 4.738 |
| r_scbond_it | 4.189 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8248 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 137 |
| Heterogen Atoms | 44 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Aimless | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
