6YJV
Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP-2-deoxy-2-fluoroglucose 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 I03 |
| Synchrotron site | Diamond |
| Beamline | I03 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2019-05-19 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.97625 |
| Spacegroup name | P 1 |
| Unit cell lengths | 46.520, 69.210, 90.650 |
| Unit cell angles | 108.42, 92.25, 106.54 |
Refinement procedure
| Resolution | 44.140 - 1.700 |
| Rwork | 0.175 |
| R-free | 0.21150 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5zic |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.588 |
| 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] | 44.140 | 1.740 |
| High resolution limit [Å] | 1.700 | 1.700 |
| Rmerge | 0.044 | 1.085 |
| Rpim | 0.028 | 0.705 |
| Number of reflections | 106002 | 7858 |
| <I/σ(I)> | 11.1 | 1 |
| Completeness [%] | 94.7 | |
| Redundancy | 3.5 | |
| CC(1/2) | 0.999 | 0.547 |
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 |
