5NPS
The human O-GlcNAc transferase in complex with a bisubstrate inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.4 | 295 | 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4 + seeds generated out of this condition |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.34 | 63 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 137.869 | α = 90 |
| b = 151.333 | β = 90 |
| c = 200.478 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | F 2 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 PILATUS3 2M | 2016-11-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.98 | ESRF | MASSIF-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rpim I (All) | 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 | 1.68 | 46.1 | 99.3 | 0.05 | 0.06 | 0.04 | 0.99 | 13 | 4.7 | 117257 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.68 | 1.71 | 99.9 | 1.285 | 1.624 | 0.979 | 0.45 | 1 | 4.8 | ||||||||||
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 | 1.68 | 46.1 | 111305 | 5933 | 99.18 | 0.1942 | 0.19277 | 0.22143 | RANDOM | 36.148 | ||||||||
| 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] | |
| -0.49 | 2.13 | -1.64 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.992 |
| r_dihedral_angle_4_deg | 17.367 |
| r_dihedral_angle_3_deg | 12.546 |
| r_dihedral_angle_1_deg | 5.416 |
| r_long_range_B_refined | 5.377 |
| r_long_range_B_other | 5.251 |
| r_scangle_other | 3.371 |
| r_mcangle_other | 2.518 |
| r_mcangle_it | 2.517 |
| r_scbond_it | 2.006 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5475 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 478 |
| Heterogen Atoms | 78 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
| Coot | model building |
