4TYM

Crystal structure of purine nucleoside phosphorylase from Streptococcus agalactiae 2603V/R, NYSGRC Target 030935

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.2 M lithium sulfate, 0.1 M Tris:HCl, pH 7.0. 2.0 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.552	α = 90
b = 156.552	β = 90
c = 52.09	γ = 120

Symmetry
Space Group	P 63 2 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	RAYONIX MX225HE		2014-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9791	APS	31-ID

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	2.2	50	88.8	0.133	7.3	3.9		32265			38.84

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	2.2	2.24	43.9		0.948		1.8	803

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.399	33.895	0.01	27786	1311	99.3	0.1677	0.1664	0.1926	51.8877

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	15.643
f_angle_d	1.088
f_chiral_restr	0.044
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1820
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	15

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	refinement
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.