Crystallographic structure of the enzymatically active N-terminal domain of the Rel protein from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1VJ7 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 0.8M succinic acid, pH 7.0, 0.2M MgCl2, 0.2-0.4M Trimethylamin-N-oxide, 20% w/v Benzamidine hydrochloride hydrate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.19 | 61.79 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 161.71 | α = 90 |
| b = 161.71 | β = 90 |
| c = 75.56 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 |
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 QUANTUM 315 | mirrors | 2017-03-07 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1 | NSRRC | BL13B1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 3.7 | 20 | 99.2 | 0.05 | 0.9874 | 15.6 | 11.1 | 23372 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 3.7 | 3.83 | 99.7 | 0.243 | 0.962 | 3.9 | 3.2 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1vj7 | 3.7 | 10.02 | 21004 | 1104 | 94.24 | 0.35105 | 0.3502 | 0.35 | 0.36765 | 0.36 | RANDOM | 107.249 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| -12.14 | -12.14 | 24.28 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 28.675 |
| r_dihedral_angle_3_deg | 14.997 |
| r_dihedral_angle_4_deg | 12.162 |
| r_dihedral_angle_1_deg | 5.396 |
| r_long_range_B_refined | 3.018 |
| r_long_range_B_other | 3.018 |
| r_angle_refined_deg | 1.162 |
| r_angle_other_deg | 0.954 |
| r_mcangle_it | 0.391 |
| r_mcangle_other | 0.391 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9446 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 3 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
