Experiment: 5NRB

A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - alpha-3GalT in complex with Co2+, UDP-Gal and lactose - a3GalT-Co2+-UDP-Gal-LAT-1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NR9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.02 M L-Na-glutamate, 0.02 M alanine (racemic), 0.02 M glycine, 0.02 M L-lysine (racemic), 0.02 M serine (racemic), 0.1 M Sodium HEPES-MOPS (acid) mix pH 7.5, 20% (v/v) glycerol and 10% (w/v) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.963	α = 90
b = 65.646	β = 102.92
c = 82.654	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M		2017-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.24	58.56	99	0.0915	0.991	9.32	3.3		33428

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.24	2.32	99		0.582	2.22	3.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5NR9	2.24	58.56	33428	1710	95.64	0.2015	0.1991	0.2065	0.2462	0.2535	Random selection

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.281
f_angle_d	0.518
f_chiral_restr	0.043
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4497
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	97

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing