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