4DAR

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with tubercidin

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
2.77	55.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.638	α = 90
b = 135.638	β = 90
c = 57.56	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 Sym 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	3.15	117.466	99.8	0.116	10.5	5.3	5743	5743

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.32	100		0.34	0.34	2	5.4	812

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	3.15	20	5713	260	99.65	0.2193	0.2168	0.2714	RANDOM	60.804

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]
-1.52	-0.76		-1.52		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.956
r_dihedral_angle_3_deg	15.758
r_dihedral_angle_4_deg	11.234
r_dihedral_angle_1_deg	5.956
r_scangle_it	1.436
r_angle_refined_deg	1.153
r_mcangle_it	0.931
r_angle_other_deg	0.856
r_scbond_it	0.776
r_mcbond_it	0.501

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.956
r_dihedral_angle_3_deg	15.758
r_dihedral_angle_4_deg	11.234
r_dihedral_angle_1_deg	5.956
r_scangle_it	1.436
r_angle_refined_deg	1.153
r_mcangle_it	0.931
r_angle_other_deg	0.856
r_scbond_it	0.776
r_mcbond_it	0.501
r_chiral_restr	0.056
r_mcbond_other	0.04
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1761
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	19

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	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.