N-acetylglucosamine 6-phosphate dehydratase: inhibited 6-phosphogluconic acid state of NagS
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 2.0 M Ammonium sulphate, 0.1 M BIS-Tris, pH 5.5; after crystallosation, crystals were soaked in mother liquor with 10-20% glycerol as cryoprotectant | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.96 | 58.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.668 | α = 90 |
| b = 87.668 | β = 90 |
| c = 278.81 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | 2019-07-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 1.69 | 46.5 | 100 | 1 | 20.9 | 19.7 | 75437 | 35.45 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.69 | 1.72 | 0.799 | 1.7 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.69 | 46.47 | 1.35 | 71889 | 3548 | 99.9 | 0.1815 | 0.1803 | 0.1817 | 0.2051 | 0.2053 | 44.88 | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.7519 |
| f_angle_d | 1.2281 |
| f_chiral_restr | 0.0817 |
| f_bond_d | 0.0148 |
| f_plane_restr | 0.013 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3626 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 181 |
| Heterogen Atoms | 44 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHASER | phasing |
