4DA0

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2'-deoxyguanosine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	291	0.1 M sodium acetate, 3.2 M sodium chloride, 5%(v/v) glycerol, pH 4.6, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.352	α = 90
b = 135.352	β = 90
c = 56.801	γ = 120

Symmetry
Space Group	P 63 2 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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2		LNLS	W01B-MX2

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	2.95	50	99.7	0.127	7.8	10		6857

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	2.95	3.06	98.3		0.51		8.5	651

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.95	44.3	6782	321	98.83	0.2308	0.2271	0.3095	RANDOM	62.8993

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	-0.04		-0.07		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.762
r_dihedral_angle_3_deg	17.561
r_dihedral_angle_4_deg	15.441
r_dihedral_angle_1_deg	6.802
r_scangle_it	1.884
r_angle_refined_deg	1.302
r_mcangle_it	1.29
r_scbond_it	1.072
r_mcbond_it	0.761
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.762
r_dihedral_angle_3_deg	17.561
r_dihedral_angle_4_deg	15.441
r_dihedral_angle_1_deg	6.802
r_scangle_it	1.884
r_angle_refined_deg	1.302
r_mcangle_it	1.29
r_scbond_it	1.072
r_mcbond_it	0.761
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1755
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

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

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.