4PG5
Crystal structure of S. aureus Homoserine Dehydrogenase at pH6.5
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.2M Magnesium acetate, 16% PEG3350, 0.1M Sodium Cacodylate, pH6.5, 5% Glycerol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.41 | 48.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.48 | α = 90 |
| b = 115.43 | β = 90 |
| c = 118.23 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | MARMOSAIC 225 mm CCD | 2012-07-29 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.95372 | ESRF | BM14 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.2 | 118.23 | 100 | 20.7 | 8.6 | 51107 | 48.4 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.2 | 2.32 | 100 | 0.492 | 0.492 | 0.177 | 1.1 | 8.5 | 7340 | ||||||||||
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 | 3DO5 | 2.2 | 38.5 | 48454 | 2588 | 100 | 0.203 | 0.201 | 0.238 | RANDOM | 36.28 | ||||||
| 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] | |
| -1.34 | 1.66 | -0.32 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.445 |
| r_dihedral_angle_4_deg | 16.827 |
| r_dihedral_angle_3_deg | 14.507 |
| r_long_range_B_other | 6.593 |
| r_long_range_B_refined | 6.589 |
| r_dihedral_angle_1_deg | 6.24 |
| r_scangle_other | 3.97 |
| r_mcangle_it | 3.716 |
| r_mcangle_other | 3.716 |
| r_scbond_it | 2.565 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5822 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 236 |
| Heterogen Atoms | 86 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-3000 | data collection |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
| Coot | model building |
| PDB_EXTRACT | data extraction |
