2YHW
High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 40% PEG 300. | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.83 | 56.57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 90.73 | α = 90 |
| b = 90.73 | β = 90 |
| c = 100.78 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 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 | CCD | MARMOSAIC 225 mm CCD | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | BESSY | 14.2 | |
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 | 1.64 | 45.3 | 100 | 0.06 | 30.66 | 12.9 | 52083 | 4.37 | |||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | OTHER | THROUGHOUT | NONE | 1.64 | 45.37 | 49478 | 2605 | 100 | 0.14933 | 0.1482 | 0.16 | 0.17019 | 0.18 | RANDOM | 25.699 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 0.39 | 0.39 | -0.79 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.213 |
| r_dihedral_angle_4_deg | 19.749 |
| r_dihedral_angle_3_deg | 14.316 |
| r_dihedral_angle_1_deg | 6.637 |
| r_scangle_it | 5.643 |
| r_scbond_it | 3.468 |
| r_mcangle_it | 2.122 |
| r_angle_refined_deg | 2.068 |
| r_mcbond_it | 1.274 |
| r_angle_other_deg | 1.184 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2271 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 255 |
| Heterogen Atoms | 71 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
