5EP8

X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis with Sulfate Ion

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	Sodium acetate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.463	α = 90
b = 91.35	β = 90
c = 109.8	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	PSI PILATUS 6M		2015-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.66	70.224	99.5	0.057	0.065	0.03	17.7	4.3	23783	23783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.66	2.8	99.7		0.891	0.891	0.468	0.9	4.4	3424

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	3H5Q	2.66	70.22	22573	1171	99.39	0.2191	0.2154	0.2928	RANDOM	75.353

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]
7.45			-4.34		-3.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.888
r_dihedral_angle_3_deg	15.651
r_dihedral_angle_4_deg	14.629
r_dihedral_angle_1_deg	5.95
r_mcangle_it	4.564
r_mcbond_it	2.785
r_mcbond_other	2.783
r_angle_refined_deg	1.125
r_angle_other_deg	0.855
r_chiral_restr	0.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.888
r_dihedral_angle_3_deg	15.651
r_dihedral_angle_4_deg	14.629
r_dihedral_angle_1_deg	5.95
r_mcangle_it	4.564
r_mcbond_it	2.785
r_mcbond_other	2.783
r_angle_refined_deg	1.125
r_angle_other_deg	0.855
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6466
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

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 R01GM133198.