4CDR
Human O-GlcNAc transferase in complex with a bisubstrate inhibitor, Goblin1
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4AY6 | PDB ENTRY 4AY6 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 9.3 | 1.45 M K2HPO4, 10 MM EDTA, 1% XYLITOL, pH 9.3 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.8 | 74 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 273.728 | α = 90 |
| b = 273.728 | β = 90 |
| c = 142.581 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 3 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 | PIXEL | DECTRIS PILATUS 6M | 2012-11-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 | |
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 | 3.15 | 30 | 99.2 | 0.14 | 9.2 | 4.3 | 104870 | 2 | |||||||||||
| 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 | 3.15 | 3.3 | 99.7 | 0.5 | 3.1 | 4.5 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4AY6 | 3.15 | 30 | 101727 | 3141 | 99.03 | 0.19746 | 0.19697 | 0.21338 | RANDOM | 54.631 | ||||||
| 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] | |
| 1.09 | 0.55 | 1.09 | -1.64 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.29 |
| r_dihedral_angle_4_deg | 18.701 |
| r_dihedral_angle_3_deg | 16.806 |
| r_dihedral_angle_1_deg | 5.633 |
| r_scangle_it | 3.311 |
| r_scbond_it | 1.803 |
| r_mcangle_it | 1.412 |
| r_angle_refined_deg | 1.343 |
| r_mcbond_it | 0.704 |
| r_chiral_restr | 0.086 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 22268 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 255 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data reduction |
| SCALA | data scaling |
| REFMAC | phasing |
