3TZX
Crystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in tetragonal apo form at 2.3 A
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2HG4 | PDB ID: 2HG4 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 285 | 0.1M HEPES, 1.7m ammonium sulfate, 15% glycerol, 1.7% PEG-400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.37 | 63.51 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 106.56 | α = 90 |
| b = 106.56 | β = 90 |
| c = 258.61 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 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 | CCD | ADSC QUANTUM 210 | 2010-04-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9334 | ESRF | ID14-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.3 | 41.7 | 96.9 | 0.067 | 4.2 | 65097 | 41.5 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.3 | 2.4 | 83.4 | 0.329 | 2.3 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID: 2HG4 | 2.3 | 41.12 | 61727 | 61727 | 3291 | 96.93 | 0.20319 | 0.20319 | 0.20017 | 0.26047 | RANDOM | 38.269 | ||||
| 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] | |
| 1.05 | 1.05 | -2.1 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.517 |
| r_dihedral_angle_4_deg | 21.991 |
| r_dihedral_angle_3_deg | 17.301 |
| r_dihedral_angle_1_deg | 6.883 |
| r_angle_refined_deg | 2.068 |
| r_chiral_restr | 0.132 |
| r_bond_refined_d | 0.019 |
| r_gen_planes_refined | 0.01 |
| r_bond_other_d | |
| r_angle_other_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7123 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 351 |
| Heterogen Atoms | 44 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DNA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
