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

X-RAY DIFFRACTION

---

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

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.6	α = 107.48
b = 69.55	β = 92.26
c = 90.94	γ = 106.22

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-F		2019-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95004	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	1.96	85.95	95.5	0.055	0.035	0.999	12.8	3.5		71053

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	1.96	2.01			1.244	0.791	0.581	1.1

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	1.96	85.95	71053	3368	95.437	0.202	0.1999	0.2523	51.702

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]
-2.859	0.183	0.84	2.288	3.094	-2.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.377
r_dihedral_angle_4_deg	18.274
r_dihedral_angle_3_deg	15.991
r_lrange_it	8.796
r_lrange_other	8.796
r_scangle_it	7.235
r_scangle_other	7.199
r_dihedral_angle_1_deg	7.139
r_mcangle_it	5.965
r_mcangle_other	5.964
r_scbond_it	5.14
r_scbond_other	5.092
r_mcbond_it	4.489
r_mcbond_other	4.489
r_angle_refined_deg	1.597
r_angle_other_deg	1.261
r_symmetry_nbd_refined	0.224
r_nbd_other	0.214
r_nbd_refined	0.204
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.138
r_ncsr_local_group_1	0.084
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8103
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	157

Software

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