Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with naproxenoyl-CoA
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8RMW | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295.15 | 4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.04 | 69.57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 276.278 | α = 90 |
| b = 276.278 | β = 90 |
| c = 389.216 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 2 2 |
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 EIGER2 X 16M | 2024-04-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.953731 | Diamond | I04 |
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 | 2 | 225.29 | 100 | 0.245 | 0.066 | 0.999 | 10.1 | 27.5 | 497035 | ||||||||||
| 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 | 10.95 | 225.29 | 100 | 0.039 | 0.008 | 1 | 39.6 | 26 | |||||||||||
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2 | 225.29 | 496995 | 24747 | 99.992 | 0.208 | 0.2062 | 0.2142 | 0.239 | 0.2464 | 44.988 | ||||||
| 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] | |
| -0.349 | -0.349 | 0.698 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 14.798 |
| r_dihedral_angle_6_deg | 14.392 |
| r_dihedral_angle_2_deg | 12.079 |
| r_lrange_other | 8.961 |
| r_lrange_it | 8.954 |
| r_dihedral_angle_1_deg | 6.969 |
| r_scangle_it | 6.807 |
| r_scangle_other | 6.807 |
| r_mcangle_it | 6.175 |
| r_mcangle_other | 6.175 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 32568 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1793 |
| Heterogen Atoms | 768 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| Coot | model building |
