4M7W | pdb_00004m7w

Crystal structure of purine nucleoside phosphorylase from Leptotrichia buccalis C-1013-b, NYSGRC Target 029767.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	0.1 M sodium acetate:acetic acid, pH 4.5, 0.8 M NaH2PO4/1.2M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.877	α = 90
b = 164.877	β = 90
c = 45.527	γ = 120

Symmetry
Space Group	P 3 2 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		2013-08-09		SAD

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	99.8	0.11	13.7	14.2		55825

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	99.6		0.366		13.2	2693

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	32.9	55501	2817	99.3	0.2035	0.2014	0.2019	0.2438	0.2448	RANDOM	34.6665

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]
-5.78			-5.78		11.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.892
r_dihedral_angle_4_deg	20.912
r_dihedral_angle_3_deg	14.563
r_dihedral_angle_1_deg	5.847
r_scbond_it	2.864
r_mcangle_it	2.636
r_mcbond_it	1.577
r_angle_refined_deg	1.409
r_chiral_restr	0.084
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.892
r_dihedral_angle_4_deg	20.912
r_dihedral_angle_3_deg	14.563
r_dihedral_angle_1_deg	5.847
r_scbond_it	2.864
r_mcangle_it	2.636
r_mcbond_it	1.577
r_angle_refined_deg	1.409
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5379
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	15

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXD	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.