Experiment: 2YFC

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YF9	PDB ENTRY 2YF9

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.28	49.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.733	α = 90
b = 150.191	β = 90
c = 52.423	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 QUANTUM 315r		2009-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	1.9	40	97.8	0.07	11.2	3.4		48355		2	20.29

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	1.9	2	93.4		0.36	2.7	2.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2YF9	2.01	20.001	1.34	41628	2082	98.63	0.1796	0.1775	0.1711	0.2188	0.211	24.56

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]
0.6835			-0.3526		-0.1906

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.079
f_angle_d	1.151
f_chiral_restr	0.069
f_bond_d	0.012
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4096
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	70

Software

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