5NJ2
Crystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2GDN | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 0.1 M sodium acetate buffer, pH 5.0, 25% PEG1500 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.15 | 42.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 39.591 | α = 101.28 |
| b = 41.683 | β = 90.11 |
| c = 76.841 | γ = 90.43 |
| Symmetry | |
|---|---|
| Space Group | P 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 | PIXEL | DECTRIS EIGER X 4M | 2016-11-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.19 | 75.36 | 62.7 | 0.063 | 0.041 | 0.998 | 11.3 | 3.2 | 96841 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.19 | 1.23 | 0.573 | 0.467 | 0.523 | 1.2 | 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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2GDN | 1.19 | 75.36 | 92053 | 4773 | 62.69 | 0.16797 | 0.16683 | 0.18953 | RANDOM | 11.803 | ||||||
| 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] | |
| -0.32 | 0.32 | 0.03 | 0.71 | -0.01 | -0.37 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.498 |
| r_dihedral_angle_4_deg | 21.668 |
| r_dihedral_angle_3_deg | 11.445 |
| r_dihedral_angle_1_deg | 6.294 |
| r_long_range_B_refined | 3.833 |
| r_long_range_B_other | 3.833 |
| r_scangle_other | 3.137 |
| r_scbond_it | 2.234 |
| r_scbond_other | 2.234 |
| r_angle_refined_deg | 2.185 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4045 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 288 |
| Heterogen Atoms | 60 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
