6YJT

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

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
2.25	45.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.03	α = 107.77
b = 69.59	β = 91.81
c = 90	γ = 106.94

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		2019-04-08	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	43.43	96	0.047	0.03	0.999	9.9	3.6		108811

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			1.346	0.804	0.562	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	43.43	104711	3727	95.643	0.186	0.1845	0.2228	54.886

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]
-3.17	1.476	1.511	1.744	3.277	-2.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.194
r_dihedral_angle_4_deg	16.022
r_dihedral_angle_3_deg	14.595
r_lrange_other	9.344
r_lrange_it	9.335
r_scangle_it	7.598
r_scangle_other	7.594
r_dihedral_angle_1_deg	7.055
r_mcangle_other	5.608
r_mcangle_it	5.607
r_scbond_it	5.149
r_scbond_other	5.121
r_mcbond_it	4.187
r_mcbond_other	4.182
r_angle_refined_deg	1.536
r_angle_other_deg	1.255
r_nbd_other	0.228
r_symmetry_xyhbond_nbd_refined	0.206
r_symmetry_nbd_refined	0.194
r_nbd_refined	0.192
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.154
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.074
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	8218
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	140

Software

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