3KGF
The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with phenylalanine and tryptophan
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 20mM BTP, 150mM NaCl, 0.5mM TCEP, 0.005%(v/v) Thesit, 0.2mM PEP, 0.1mM MnCl2, 0.1M Na HEPES, 0.8M NaK phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.95 | 68.84 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 204.537 | α = 90 |
| b = 204.537 | β = 90 |
| c = 66.462 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 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 | 120 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic Blue Mirrors | 2005-12-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.542 | ||
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 | 2 | 39.5 | 98.2 | 0.064 | 8.2 | 2.07 | 105425 | 105425 | 37.5 | ||||||||||
| 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 | 2 | 2.07 | 87.2 | 0.381 | 2.1 | 2.38 | 10487 | ||||||||||||
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 | 2b7o | 2 | 32.67 | 105110 | 105110 | 5245 | 97.91 | 0.16423 | 0.164 | 0.163 | 0.191 | RANDOM | 25.418 | ||||
| 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] | |
| -0.15 | -0.08 | -0.15 | 0.23 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.003 |
| r_dihedral_angle_4_deg | 15.749 |
| r_dihedral_angle_3_deg | 12.893 |
| r_dihedral_angle_1_deg | 6.187 |
| r_scangle_it | 4.212 |
| r_scbond_it | 2.796 |
| r_angle_refined_deg | 1.318 |
| r_mcangle_it | 1.09 |
| r_angle_other_deg | 0.976 |
| r_mcbond_it | 0.696 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6976 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 771 |
| Heterogen Atoms | 191 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrystalClear | data collection |
| CCP4 | model building |
| REFMAC | refinement |
| d*TREK | data reduction |
| d*TREK | data scaling |
| CCP4 | phasing |
