6YJU
Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP and biantennary pentasaccharide M592
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04 |
Synchrotron site | Diamond |
Beamline | I04 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-03-02 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.95004 |
Spacegroup name | P 1 |
Unit cell lengths | 46.600, 69.550, 90.940 |
Unit cell angles | 107.48, 92.26, 106.22 |
Refinement procedure
Resolution | 85.950 - 1.960 |
Rwork | 0.200 |
R-free | 0.25230 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5zic |
RMSD bond length | 0.009 |
RMSD bond angle | 1.597 |
Data reduction software | xia2 |
Data scaling software | xia2 |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 85.950 | 2.010 |
High resolution limit [Å] | 1.960 | 1.960 |
Rmerge | 0.055 | 1.244 |
Rpim | 0.035 | 0.791 |
Number of reflections | 71053 | 5324 |
<I/σ(I)> | 12.8 | 1.1 |
Completeness [%] | 95.5 | |
Redundancy | 3.5 | |
CC(1/2) | 0.999 | 0.581 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1 M HEPES pH 8.0, 0.3 M Li2SO4, 30 % (w/v) PEG 3350, 10 % (v/v) ethylene glycol |