2YFD

STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH Mg and dUMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.18 M LITHIUM ACETATE, 20% (W/V) PEG 3350, 10MM DUTP, 10MM MAGNESIUM CHLORIDE.

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.09	α = 90
b = 149.529	β = 90
c = 52.376	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	CCD	ADSC CCD		2009-12-03	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.77	49.84	94.3	0.07	17.2	5.1		57356		2	18.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.86	75		0.46	3.1	4.1

Refinement

Statistics
Diffraction ID	Structure Solution 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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2YF9	1.767	19.934	1.36	57235	2861	93.92	0.1857	0.1843	0.2114	22.06

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]
4.3761			-1.2161		-3.16

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.378
f_angle_d	1.058
f_chiral_restr	0.073
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4106
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	60

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.