6YJS
Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 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] | 293 |
| Detector technology | PIXEL |
| Collection date | 2019-02-15 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.9795 |
| Spacegroup name | P 1 |
| Unit cell lengths | 46.280, 67.370, 91.050 |
| Unit cell angles | 108.81, 92.20, 106.72 |
Refinement procedure
| Resolution | 42.520 - 1.600 |
| Rwork | 0.184 |
| R-free | 0.21450 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5zic |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.620 |
| 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] | 42.520 | 1.640 |
| High resolution limit [Å] | 1.600 | 1.600 |
| Rmerge | 0.054 | 1.162 |
| Rpim | 0.034 | 0.722 |
| Number of reflections | 125194 | 9094 |
| <I/σ(I)> | 10.4 | 1.2 |
| Completeness [%] | 96.2 | |
| Redundancy | 3.5 | |
| CC(1/2) | 0.999 | 0.524 |
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 wXHPcQHrME |
