7ERX

Glycosyltransferase in complex with UDP and STB

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM HEPES-NaOH buffer pH 6.5 and 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.482	α = 90
b = 83.173	β = 90
c = 109.391	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

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	1.92	109.39	99.7	0.055	0.066	0.036	0.999	14.5	6.2		38620

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	1.92	1.97			1.852	2.264	1.282	0.626		5.1

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	THROUGHOUT	7ERY	1.92	66.297	38555	1952	99.564	0.19	0.1885	0.2135	48.917

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]
4.769			-1.981		-2.788

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.958
r_dihedral_angle_3_deg	14.027
r_dihedral_angle_4_deg	12.971
r_dihedral_angle_1_deg	6.845
r_lrange_it	4.643
r_lrange_other	4.643
r_dihedral_angle_other_2_deg	3.456
r_scangle_it	2.951
r_scangle_other	2.95
r_mcangle_it	2.419
r_mcangle_other	2.418
r_scbond_it	1.87
r_scbond_other	1.869
r_mcbond_it	1.547
r_mcbond_other	1.547
r_angle_refined_deg	1.477
r_angle_other_deg	1.283
r_symmetry_nbd_refined	0.24
r_nbd_refined	0.203
r_nbd_other	0.188
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.048
r_symmetry_xyhbond_nbd_refined	0.041
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3089
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
DIALS	data reduction
PHASER	phasing
DIALS	data scaling