5NPR
The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID29 |
Synchrotron site | ESRF |
Beamline | ID29 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2014-07-05 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.976 |
Spacegroup name | F 2 2 2 |
Unit cell lengths | 138.038, 150.951, 200.540 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 46.010 - 1.850 |
R-factor | 0.2065 |
Rwork | 0.205 |
R-free | 0.23641 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3pe4 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.408 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.15) |
Phasing software | MOLREP (11.4.03) |
Refinement software | REFMAC (5.8.0155) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 46.010 | 1.880 |
High resolution limit [Å] | 1.850 | 1.850 |
Rmerge | 0.060 | 0.871 |
Rpim | 0.048 | 0.711 |
Number of reflections | 88158 | |
<I/σ(I)> | 9.7 | 1.3 |
Completeness [%] | 99.5 | 99.8 |
Redundancy | 4 | 4.1 |
CC(1/2) | 0.990 | 0.650 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.4 | 295 | Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds Seeds were generated from crystals grown in 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4 |