5MX8

Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	291	0.2M NaCl, 0.1M Na/K phosphate pH 6.2, 50% PEG 200

Crystal Properties
Matthews coefficient	Solvent content
4.78	74.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.596	α = 90
b = 143.596	β = 90
c = 143.596	γ = 90

Symmetry
Space Group	P 41 3 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	OXFORD RUBY CCD		2015-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.541

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	2.4	29.311	99.4	15.2	14		20243

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	5MX4	2.4	29.311	1.33	20237	1002	99.36	0.2158	0.2135	0.2591	37.169

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	16.352
f_angle_d	1.063
f_chiral_restr	0.056
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1802
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	113

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
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 R01GM157729.