8OVS

Crystal structure of YeGT glycosyltransferase with bound UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MIX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100mM HEPES pH 7.5, 500mM sodium acetate, 50mM cadmium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.13	α = 90
b = 114.546	β = 89.987
c = 69.376	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 PILATUS 6M		2017-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0000	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.12	47.13	92.7	0.132	0.023	0.999	18	30.3		213705

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.12	1.22			2.038	0.479	0.39	1.7	18.4

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	1.123	47.13	213699	10763	76.61	0.154	0.1533	0.1685	17.643

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]
-8.967		-0.612	13.568		-4.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.982
r_dihedral_angle_other_3_deg	18.238
r_dihedral_angle_4_deg	17.08
r_dihedral_angle_3_deg	11.238
r_dihedral_angle_1_deg	5.678
r_lrange_it	2.748
r_lrange_other	2.046
r_angle_other_deg	1.231
r_angle_refined_deg	1.196
r_mcangle_it	1.157
r_mcangle_other	1.156
r_scangle_it	1.146
r_scangle_other	1.146
r_scbond_it	1.036
r_scbond_other	0.96
r_mcbond_it	0.832
r_mcbond_other	0.829
r_rigid_bond_restr	0.714
r_nbd_refined	0.184
r_symmetry_nbd_other	0.167
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.143
r_nbd_other	0.12
r_metal_ion_refined	0.117
r_xyhbond_nbd_refined	0.104
r_symmetry_xyhbond_nbd_refined	0.094
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.058
r_symmetry_metal_ion_refined	0.058
r_chiral_restr	0.055
r_bond_other_d	0.01
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4369
Nucleic Acid Atoms
Solvent Atoms	871
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
autoPROC	data processing
PHASER	phasing
STARANISO	data scaling
Coot	model building
autoPROC	data reduction