Experiment: 8HJL

Crystal structure of glycosyltransferase SgUGT94-289-3 in complex with M3E

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8HJP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	Tris-HCl, polyethylene glycol 3350, NaCl, Polypropylene glycol P400.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.633	α = 90
b = 76.161	β = 92.59
c = 82.254	γ = 90

Symmetry
Space Group	P 1 21 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		2020-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97918	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.72	50	90.88	0.998	25.55	6.5		101044			13.19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.071			0.998

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6JTD	1.72	24.63	1.34	101043	4757	97.67	0.2125	0.2104	0.2098	0.2552	0.2541	20.05

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	14.9333
f_angle_d	1.0794
f_chiral_restr	0.3682
f_plane_restr	0.0073
f_bond_d	0.0067

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6810
Nucleic Acid Atoms
Solvent Atoms	1250
Heterogen Atoms	438

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
AutoProcess	data processing
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data reduction