Experiment: 7OPA

Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzylthiopurine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6F4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294.15	12% PEG 8000, Tris-HCl pH 7,0

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.56	α = 90
b = 138.998	β = 90
c = 318.723	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2021-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.00	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	49.62	99.7	0.181	0.189	0.997	9.79	12.3		204075		-3	36.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.12	98.6		1.902	2.003	0.637	0.89

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6F4X	2	49.62	1.36	202856	1999	99.84	0.2293	0.2288	0.2291	0.2854	0.2861	44.8743

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21616
Nucleic Acid Atoms
Solvent Atoms	1057
Heterogen Atoms	180

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing