8CE3

Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548

X-RAY DIFFRACTION

---

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	45.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.86	α = 107.3
b = 68.54	β = 92.16
c = 91.31	γ = 107.05

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 EIGER X 16M		2019-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.89	60.47	97.26	0.047	1	13.6	3.5		80017

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.92			1.297	0.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.89	60.465	80017	3795	97.259	0.192	0.1897	0.2327	54.819

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]
-0.258	1.025	0.567	-0.062	1.78	-1.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.501
r_dihedral_angle_3_deg	15.187
r_lrange_it	10.513
r_lrange_other	10.512
r_scangle_it	9.087
r_scangle_other	9.087
r_dihedral_angle_1_deg	6.898
r_mcangle_it	6.839
r_mcangle_other	6.839
r_scbond_it	6.459
r_scbond_other	6.459
r_dihedral_angle_2_deg	6.242
r_mcbond_it	5.456
r_mcbond_other	5.456
r_angle_refined_deg	1.51
r_angle_other_deg	0.487
r_xyhbond_nbd_refined	0.265
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.197
r_nbd_other	0.19
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.176
r_symmetry_xyhbond_nbd_other	0.137
r_ncsr_local_group_1	0.102
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.074
r_gen_planes_refined	0.009
r_bond_refined_d	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	8033
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	112

Software

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