4M1E

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.1 M MES:NaOH, pH 6.5, 1.6 Magnesium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.95	α = 103.42
b = 81.06	β = 105.36
c = 91.616	γ = 112.73

Symmetry
Space Group	P 1

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		2013-07-18		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	1.9	50	97	0.113	9.7	2.1		148934

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	1.93	94.3		0.718		2	7253

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3LA8	1.9	20	146913	7374	97.07	0.2154	0.2132	0.2575	RANDOM	34.4156

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]
-0.07	0.66	0.46	-0.26	0.78	-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.245
r_dihedral_angle_4_deg	20.427
r_dihedral_angle_3_deg	15.844
r_dihedral_angle_1_deg	5.751
r_scbond_it	2.72
r_mcangle_it	2.644
r_mcbond_it	1.624
r_angle_refined_deg	1.424
r_chiral_restr	0.093
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.245
r_dihedral_angle_4_deg	20.427
r_dihedral_angle_3_deg	15.844
r_dihedral_angle_1_deg	5.751
r_scbond_it	2.72
r_mcangle_it	2.644
r_mcbond_it	1.624
r_angle_refined_deg	1.424
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12435
Nucleic Acid Atoms
Solvent Atoms	662
Heterogen Atoms	144

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.