9F5H

Crystal structure of MGAT5 bump-and-hole mutant in complex with UDP and M592

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YJR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	15-20% PEG3350, 0.1M Tris-HCl pH 8-8.5, 0.3M Li2SO4, 0-10% ethylene glycol, Microseed matrix screening

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.507	α = 108.208
b = 69.069	β = 92.088
c = 90.993	γ = 106.747

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 EIGER2 XE 16M		2023-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.72738	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.97	44.1	94.4	0.116	0.164	0.116	0.994	6.6	3.8		68392

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.01			1.557	2.2	1.554	0.27		3.8

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	THROUGHOUT	1.97	44.1	68300	3266	94.644	0.202	0.1996	0.2418	38.744

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]
0.475	-0.48	-1.014	0.507	0.172	-0.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.255
r_dihedral_angle_3_deg	14.72
r_dihedral_angle_2_deg	13.407
r_dihedral_angle_1_deg	7.351
r_lrange_it	6.435
r_lrange_other	6.424
r_scangle_it	4.219
r_scangle_other	4.196
r_mcangle_it	3.796
r_mcangle_other	3.795
r_scbond_it	2.748
r_scbond_other	2.732
r_mcbond_it	2.458
r_mcbond_other	2.458
r_angle_refined_deg	2.139
r_angle_other_deg	0.746
r_xyhbond_nbd_refined	0.315
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.194
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.177
r_nbd_other	0.171
r_ncsr_local_group_1	0.108
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8018
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	106

Software

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