3IX2

CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ACYCLOVIR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N3I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM Tris, pH 8.0, 25%PEG 3350, and 25 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.177	α = 90
b = 135.759	β = 90
c = 41.434	γ = 90

Symmetry
Space Group	P 21 21 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	MAR scanner 300 mm plate		2009-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	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	2.1	33.94	90	0.08	0.08	10	7	39559	35559	2	2	20

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)
	2.1	2.2	90		0.2	0.2	3	4	2200

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	1N3I	2.1	33.94	2	2	35559	31718	1679	93.92	0.18653	0.18653	0.18256	0.26197	RANDOM	23.187

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	35.267
r_dihedral_angle_4_deg	21.6
r_dihedral_angle_3_deg	18.374
r_dihedral_angle_1_deg	8.139
r_scangle_it	4.722
r_scbond_it	3.124
r_mcangle_it	2.923
r_angle_refined_deg	2.388
r_mcbond_it	1.946
r_symmetry_vdw_refined	0.341

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.267
r_dihedral_angle_4_deg	21.6
r_dihedral_angle_3_deg	18.374
r_dihedral_angle_1_deg	8.139
r_scangle_it	4.722
r_scbond_it	3.124
r_mcangle_it	2.923
r_angle_refined_deg	2.388
r_mcbond_it	1.946
r_symmetry_vdw_refined	0.341
r_nbtor_refined	0.326
r_chiral_restr	0.292
r_nbd_refined	0.267
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.19
r_bond_refined_d	0.022
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5688
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	63

Software

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

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.