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

X-RAY DIFFRACTION

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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

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.52	α = 108.42
b = 69.21	β = 92.25
c = 90.65	γ = 106.54

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	100	PIXEL	DECTRIS PILATUS 6M		2019-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.7	44.14	94.7	0.044	0.028	0.999	11.1	3.5		106002

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	1.7	1.74			1.085	0.705	0.547	1

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	1.7	44.14	106001	3663	94.657	0.177	0.1754	0.2115	43.149

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]
-2.177	0.272	-0.545	1.371	1.706	-0.719

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.923
r_dihedral_angle_4_deg	17.603
r_dihedral_angle_3_deg	15.265
r_lrange_other	8.394
r_lrange_it	8.392
r_dihedral_angle_1_deg	7.07
r_scangle_other	6.572
r_scangle_it	6.569
r_mcangle_it	4.733
r_mcangle_other	4.733
r_scbond_it	4.312
r_scbond_other	4.299
r_mcbond_it	3.457
r_mcbond_other	3.456
r_angle_refined_deg	1.588
r_angle_other_deg	1.274
r_symmetry_nbd_refined	0.233
r_nbd_other	0.225
r_symmetry_xyhbond_nbd_refined	0.209
r_nbd_refined	0.202
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.163
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.072
r_bond_refined_d	0.009
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	8127
Nucleic Acid Atoms
Solvent Atoms	509
Heterogen Atoms	184

Software

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