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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZIC

Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.28	α = 108.81
b = 67.37	β = 92.2
c = 91.05	γ = 106.72

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M-F		2019-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	42.52	96.2	0.054	0.034	0.999	10.4	3.5		125194

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64			1.162	0.722	0.524	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5zic	1.6	42.52	125193	3770	96.191	0.185	0.1841	0.2145	34.716

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.394	1.502	-0.052	2.302	-0.13	-2.354

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.234
r_dihedral_angle_4_deg	18.091
r_dihedral_angle_3_deg	14.646
r_lrange_it	8.288
r_lrange_other	8.258
r_dihedral_angle_1_deg	6.756
r_scangle_it	6.605
r_scangle_other	6.603
r_scbond_it	4.24
r_mcangle_it	4.224
r_mcangle_other	4.224
r_scbond_other	4.219
r_mcbond_it	2.888
r_mcbond_other	2.888
r_angle_refined_deg	1.62
r_angle_other_deg	1.291
r_nbd_other	0.242
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.167
r_symmetry_nbtor_other	0.087
r_ncsr_local_group_1	0.087
r_xyhbond_nbd_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7738
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	246

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing