6YJT
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
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-04-08 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97625 |
Spacegroup name | P 1 |
Unit cell lengths | 47.030, 69.590, 90.000 |
Unit cell angles | 107.77, 91.81, 106.94 |
Refinement procedure
Resolution | 43.430 - 1.700 |
Rwork | 0.184 |
R-free | 0.22280 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5zic |
RMSD bond length | 0.008 |
RMSD bond angle | 1.536 |
Data reduction software | xia2 |
Data scaling software | xia2 |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 43.430 | 1.740 |
High resolution limit [Å] | 1.700 | 1.700 |
Rmerge | 0.047 | 1.346 |
Rpim | 0.030 | 0.804 |
Number of reflections | 108811 | 8076 |
<I/σ(I)> | 9.9 | 1 |
Completeness [%] | 96.0 | |
Redundancy | 3.6 | |
CC(1/2) | 0.999 | 0.562 |
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 |