5D05
Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Lys107Ala variant regulated
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 296 | 0.1M Tris HCl (pH 7.3), 0.2 M trimethyl-amino-N-oxide (TMAO), 0.4 mM MnSO4 and PEG 2000MME |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.64 | 53.38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 75.331 | α = 90 |
| b = 141.027 | β = 97.02 |
| c = 76.028 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | CCD | ADSC QUANTUM 315r | 2015-07-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.954 | Australian Synchrotron | MX2 |
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 | 1.75 | 74.46 | 100 | 0.079 | 16.9 | 7.6 | 158105 | ||||||||||||
| 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 | 1.75 | 1.78 | 99.7 | 0.869 | 2.2 | 7.4 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 1.75 | 74.46 | 148147 | 9914 | 99.98 | 0.15118 | 0.14953 | 0.17564 | RANDOM | 24.327 | ||||||||
| 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] | |
| 0.58 | -0.23 | 0.09 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.561 |
| r_dihedral_angle_4_deg | 14.319 |
| r_dihedral_angle_3_deg | 12.268 |
| r_dihedral_angle_1_deg | 5.517 |
| r_long_range_B_refined | 5.098 |
| r_long_range_B_other | 5.098 |
| r_scangle_other | 2.4 |
| r_scbond_it | 1.545 |
| r_scbond_other | 1.545 |
| r_angle_refined_deg | 1.387 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10598 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1132 |
| Heterogen Atoms | 146 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
