3M7W
Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Covalent Complex with Dehydroquinate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.6 | 295 | Protein solution: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate (pH 4.6), 25.5% PEG 4000, 15% Glycerol; Soak: 5mM Dehydroquinic acid in screen solution for 20 min., VAPOR DIFFUSION, SITTING DROP, temperature 295K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.07 | 40.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 184.334 | α = 90 |
| b = 66.576 | β = 119.08 |
| c = 128.23 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | 100 | CCD | MARMOSAIC 225 mm CCD | BERYLLIUM LENSES | 2010-03-08 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | APS | 21-ID-F | |
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 | 1.95 | 30 | 100 | 0.086 | 14.9 | 3.7 | 99121 | -3 | 20.2 | ||||||||||
| 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) | |||||||||||
| 1.95 | 2.02 | 100 | 0.466 | 2.8 | 3.6 | ||||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3L2I | 1.95 | 29.69 | 94167 | 94167 | 4942 | 99.9 | 0.157 | 0.154 | 0.206 | RANDOM | 20.01 | |||||
| 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] | |
| 1.71 | 1.6 | -1.44 | 1.29 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.909 |
| r_dihedral_angle_4_deg | 11.719 |
| r_dihedral_angle_3_deg | 10.061 |
| r_scangle_it | 4.994 |
| r_scbond_it | 3.07 |
| r_dihedral_angle_1_deg | 3.054 |
| r_mcangle_it | 1.936 |
| r_angle_refined_deg | 1.447 |
| r_mcbond_it | 1.137 |
| r_angle_other_deg | 0.862 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11462 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1108 |
| Heterogen Atoms | 156 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Blu-Ice | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
