6YJQ

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation

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

Crystal Properties
Matthews coefficient	Solvent content
1.55	20.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47	α = 108.36
b = 68.17	β = 92.28
c = 90.99	γ = 106.86

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		2019-01-22	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	1.9	43.31	97	0.066	0.042	0.997	9.9	3.5		77533

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	1.9	1.95			1.159	0.721	0.422	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	1.9	43.31	77533	3684	96.94	0.196	0.1941	0.2371	46.468

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]
-0.211	0.557	0.304	1.185	1.592	-2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.22
r_dihedral_angle_4_deg	17.018
r_dihedral_angle_3_deg	14.703
r_lrange_it	7.646
r_lrange_other	7.624
r_dihedral_angle_1_deg	6.834
r_scangle_it	6.132
r_scangle_other	6.113
r_mcangle_it	4.795
r_mcangle_other	4.794
r_scbond_it	4.163
r_scbond_other	4.132
r_mcbond_it	3.599
r_mcbond_other	3.598
r_angle_refined_deg	1.457
r_angle_other_deg	1.252
r_symmetry_nbd_refined	0.206
r_nbd_refined	0.199
r_nbd_other	0.195
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.115
r_ncsr_local_group_1	0.088
r_symmetry_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7989
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	96

Software

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