8XM4
Methionyl-tRNA synthetase from Staphylococcus aureus in complex with chlorhexidine and ATP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 289 | 0.10 M magnesium acetate, 0.1 M Bis-Tris pH 7.0, 20% w/v PEG 3,350 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.48 | 50.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 65.409 | α = 90 |
| b = 76.059 | β = 90 |
| c = 119.046 | 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 PILATUS3 6M | 2023-03-27 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.9785 | SSRF | BL19U1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.67 | 64.09 | 96 | 0.034 | 0.038 | 0.016 | 1 | 25.8 | 5.8 | 66315 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.67 | 1.76 | 98.6 | 0.642 | 0.703 | 0.283 | 0.88 | 6 | |||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.67 | 64.09 | 62873 | 3394 | 95.71 | 0.18945 | 0.18811 | 0.21427 | RANDOM | 32.846 | |||||||
| 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] | |
| 0.07 | 1.54 | -1.61 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.717 |
| r_dihedral_angle_4_deg | 13.024 |
| r_dihedral_angle_3_deg | 11.782 |
| r_dihedral_angle_1_deg | 5.379 |
| r_long_range_B_refined | 3.415 |
| r_long_range_B_other | 3.24 |
| r_scangle_other | 1.772 |
| r_mcangle_it | 1.71 |
| r_mcangle_other | 1.71 |
| r_angle_refined_deg | 1.291 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4204 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 312 |
| Heterogen Atoms | 81 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| autoPROC | data scaling |
| MOLREP | phasing |
| autoPROC | data reduction |
| autoPROC | data scaling |
