8SFY | pdb_00008sfy

Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with UDP-glucose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	5% Tacsimate pH 7, 0.1 M HEPES pH 7, 10% PEG 5000. Protein soaked in UDP-glucose

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.231	α = 90
b = 77.231	β = 90
c = 164.197	γ = 90

Symmetry
Space Group	P 41 21 2

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		2021-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.000	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.35	40	95.9	0.113	0.046	18.6	5.3		20661		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.39	97.9		0.749	0.319	2.4	5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	38.688	20544	1047	95.651	0.22	0.2178	0.22	0.2688	0.27	37.852

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]
-0.703			-0.703		1.405

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.464
r_dihedral_angle_4_deg	23.736
r_dihedral_angle_3_deg	14.753
r_dihedral_angle_1_deg	6.996
r_lrange_it	4.357
r_lrange_other	4.337
r_scangle_it	2.567
r_scangle_other	2.566
r_mcangle_it	2.236
r_mcangle_other	2.236
r_scbond_it	1.519
r_scbond_other	1.518
r_angle_refined_deg	1.453
r_mcbond_it	1.334
r_mcbond_other	1.331
r_angle_other_deg	1.261
r_symmetry_nbd_refined	0.253
r_nbd_other	0.234
r_nbd_refined	0.201
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3323
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
SERGUI	data collection