4UC0

Crystal Structure Of a purine nucleoside phosphorylase (PSI-NYSGRC-029736) from Agrobacterium vitis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.16M MgCl2, 0.08M Tris-HCl pH 8.5, 24% PEG 4000, 20% glycerol - MCSG1 #22); Cryoprotection (None)

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.881	α = 90
b = 97.881	β = 90
c = 46.356	γ = 120

Symmetry
Space Group	P 63

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	MIRRORS	2013-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	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	2.4	50	99.5	0.093	11.2	11		19502		-3	48.4

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	2.4	2.44	100		0.942	3.1	10.3	997

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.4	20	10039	519	99.42	0.1816	0.1791	0.2241	RANDOM	59.631

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]
-0.42	-0.21		-0.42		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.309
r_dihedral_angle_4_deg	17.888
r_dihedral_angle_3_deg	14.803
r_dihedral_angle_1_deg	5.931
r_mcangle_it	3.036
r_mcbond_it	1.929
r_mcbond_other	1.913
r_angle_refined_deg	1.361
r_angle_other_deg	0.744
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.309
r_dihedral_angle_4_deg	17.888
r_dihedral_angle_3_deg	14.803
r_dihedral_angle_1_deg	5.931
r_mcangle_it	3.036
r_mcbond_it	1.929
r_mcbond_other	1.913
r_angle_refined_deg	1.361
r_angle_other_deg	0.744
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1806
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-3000	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
REFMAC	refinement

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.