3IOM

Crystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in complex with 2'-Deoxyguanosine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	The protein was cocrystallized with a 1:0.5:1 stoichiometry of 500 mM Na2SO4 (Merck) and 3 mM 2dGuo (Fluka Biochemika), respectively, by hanging-drop vapor diffusion at 18 C. MtPNP protein (1 L of 25 mg mL-1 in 50 mM tris(hydroxymethyl)aminomethane (Tris) pH 7.6) had been previously mixed with an equal volume of the reservoir solution containing 100 mM Tris pH 8.0, 25% poly(ethylene glycol) (PEG) 3350, and 25 mM MgCl2 and hanging drops (3.5 L) were equilibrated against 400 L of the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.48	α = 90
b = 113.48	β = 90
c = 85.011	γ = 120

Symmetry
Space Group	H 3

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	MAR CCD 165 mm		2009-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.42800	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.14	28.69	96.9	0.086	0.086	5.9	6.8	22411	22163	2	2	21.642

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	2.15	2.27	81.8		0.138	0.138	3.5	6.4	625

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1G2O	2.14	28.34	2	2	22163	21023	1134	98.89	0.1792	0.1792	0.17545	0.24894	RANDOM	18.181

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.75
r_dihedral_angle_4_deg	20.874
r_dihedral_angle_3_deg	16.849
r_dihedral_angle_1_deg	7.205
r_scangle_it	4.563
r_scbond_it	2.904
r_angle_refined_deg	1.976
r_mcangle_it	1.78
r_mcbond_it	1.023
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.75
r_dihedral_angle_4_deg	20.874
r_dihedral_angle_3_deg	16.849
r_dihedral_angle_1_deg	7.205
r_scangle_it	4.563
r_scbond_it	2.904
r_angle_refined_deg	1.976
r_mcangle_it	1.78
r_mcbond_it	1.023
r_nbtor_refined	0.319
r_nbd_refined	0.252
r_symmetry_vdw_refined	0.237
r_symmetry_hbond_refined	0.207
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.118
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3792
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.