Experiment: 5GN2

Crystal structure of Uracil DNA glycosylase (BdiUNG) from Bradyrhizobium diazoefficiens

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	291	20% PEG3350, 200 mM sodium citrate, 100 mM sodium citrate/citric acid

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.652	α = 90
b = 90.031	β = 90
c = 255.671	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	93	CCD	ADSC QUANTUM 270		2016-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.952	30.524	98.71	13.34	4		117654

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		FREE R-VALUE	1.952	30.524	1.33	117654	1994	98.71	0.2462	0.2455	0.2514	0.2898	0.2893

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	12.682
f_angle_d	1.256
f_chiral_restr	0.055
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8396
Nucleic Acid Atoms
Solvent Atoms	567
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement