3NVT
1.95 Angstrom crystal structure of a bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase (aroA) from Listeria monocytogenes EGD-e
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.5 | 295 | Crystals grew from The Classics screen condition 68 (F8). Protein at 7.5 mg/mL in 10 mM Tris/HCl pH 8.3 0.5 M NaCl, 5 mM BME, 1 mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.36 | 47.79 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 111.57 | α = 90 |
| b = 111.787 | β = 127.63 |
| c = 81.049 | 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 300 mm CCD | BE LENSES/DIAMOND LAUE MONO | 2010-06-30 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | APS | 21-ID-G | |
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 | 99.8 | 0.097 | 105.69 | 3.1 | 57343 | -3 | |||||||||||
| 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 | 1.95 | 1.98 | 100 | 0.554 | 2.7 | 3.1 | |||||||||||||
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 | 2D8D (N-TERMINAL DOMAIN) AND 1RZM (C-TERMINAL DOMAIN) | 1.95 | 29.04 | 54397 | 54397 | 2907 | 99.5 | 0.156 | 0.154 | 0.198 | RANDOM | 43.561 | |||||
| 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] | |
| 0.93 | 0.1 | -0.25 | -0.55 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.327 |
| r_dihedral_angle_4_deg | 13.962 |
| r_dihedral_angle_3_deg | 10.011 |
| r_scangle_it | 3.635 |
| r_dihedral_angle_1_deg | 2.901 |
| r_scbond_it | 2.186 |
| r_mcangle_it | 1.261 |
| r_angle_refined_deg | 1.254 |
| r_angle_other_deg | 0.785 |
| r_mcbond_it | 0.683 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5173 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 756 |
| Heterogen Atoms | 10 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Blu-Ice | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
