2VVT
Glutamate Racemase (MurI) from E. faecalis in complex with a 9-Benzyl Purine inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | PROTEIN FORMULATED AT 10 MG/ML WITH 200MM AMMONIUM ACETATE PH 7.4, 5MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 0.2 MM MGCL2 AND 20-25% PEG 3350, 100 MM TRIS PH 7.5, 20% GLYCEROL | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 39 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.402 | α = 90 |
| b = 69.432 | β = 90 |
| c = 165.12 | 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 | ADSC CCD | 2004-06-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 1.65 | 81.65 | 96.1 | 0.08 | 4.6 | 3.5 | 205055 | 2 | |||||||||||
| 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 | 1.65 | 1.69 | 99.9 | 0.13 | 5.1 | 3.6 | |||||||||||||
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 | PDB ENTRY 2JFO | 1.65 | 81.65 | 56198 | 3003 | 94.8 | 0.152 | 0.15 | 0.184 | RANDOM | 11.57 | ||||||
| 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] | |
| 0.66 | -0.49 | -0.17 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.771 |
| r_dihedral_angle_4_deg | 14.686 |
| r_dihedral_angle_3_deg | 12.159 |
| r_dihedral_angle_1_deg | 5.386 |
| r_scangle_it | 3.694 |
| r_scbond_it | 2.426 |
| r_mcangle_it | 1.475 |
| r_angle_refined_deg | 1.461 |
| r_mcbond_it | 1.047 |
| r_angle_other_deg | 0.92 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4049 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 703 |
| Heterogen Atoms | 84 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
