Experiment: 6LLW

Crystal Structure of Fagopyrum esculentum M UGT708C1 complexed with UDP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ACV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2M ammonium sulfate, 0.1M MES pH 7.0, 26.5%(w/v) polyethylene glycol 5000, 26%(w/v) benzamidine hydrochloride, 5mM UDP

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.308	α = 90
b = 144.105	β = 90
c = 69.808	γ = 90

Symmetry
Space Group	P 21 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 PILATUS3 S 6M		2018-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9789	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.25	50	99.6	0.098	0.107	0.042	13.6	6.5		47227

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	2.25	2.29	99.7		0.247	0.271	0.11	0.965		5.9

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	THROUGHOUT	2ACV	2.256	40.19	1.34	46648	2356	98.25	0.1727	0.1705	0.1757	0.2152	0.2155	35.8397

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	6.125
f_angle_d	1.068
f_chiral_restr	0.066
f_bond_d	0.008
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6642
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	50

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing