2V0G
LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A tRNA(leu) transcript with 5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1- BENZOXABOROLE (AN2690) forming an adduct to the ribose of adenosine- 76 in the enzyme editing site.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2BYT | PDB ENTRY 2BYT |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5MG/ML LEUCYL-TRNA SYNTHETASE, MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5MM L-LEUCINE, 15MM MGCL2, 50MM MES PH6.5, 0.8M AMMONIUM SULPHATE AGAINST RESERVOIR CONTAINING 1.5M AMMONIUM SULPHATE AND 0.1M MES PH6.5 | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.9 | 68 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 202.05 | α = 90 |
| b = 125.8 | β = 118.71 |
| c = 173.2 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 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 CCD | 2006-03-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 3.5 | 50 | 94.9 | 0.12 | 9 | 3 | 138057 | ||||||||||||
| 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 | 3.5 | 3.6 | 96.8 | 0.45 | 2.69 | 2.95 | |||||||||||||
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 | PDB ENTRY 2BYT | 3.5 | 152.5 | 43437 | 2324 | 95.1 | 0.249 | 0.245 | 0.314 | RANDOM | 66.29 | ||||||
| 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] | |
| 12.08 | 7.82 | -4.06 | -0.5 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.067 |
| r_dihedral_angle_3_deg | 18.442 |
| r_dihedral_angle_4_deg | 15.456 |
| r_dihedral_angle_1_deg | 6.516 |
| r_scangle_it | 1.349 |
| r_angle_refined_deg | 1.335 |
| r_angle_other_deg | 0.873 |
| r_mcangle_it | 0.715 |
| r_scbond_it | 0.682 |
| r_mcbond_it | 0.669 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14244 |
| Nucleic Acid Atoms | 3286 |
| Solvent Atoms | |
| Heterogen Atoms | 74 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
