3SCZ

Combining crystallographic, thermodynamic, and molecular dynamics studies of Mycobacterium tuberculosis purine nucleoside phosphorylase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	MtPNP:INO:SO4 and MtPNP:HX were crystallized using the experimental conditions described elsewhere. PNP solution was concentrated to 25 mg/mL and co-crystallized with INO:SO4 and HX. Hanging drops were prepared mixing 1 uL of protein solution and 1 uL of reservoir solution (100 mM Tris, pH 8.0, 25 % PEG3350, 25 mM MgCl2), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.59	α = 90
b = 115.59	β = 90
c = 86.3	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	MARMOSAIC 325 mm CCD		2010-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.431	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	1.95	21.09	100	0.099	0.099				31352	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	100

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	1.95	21.09	29751	1578	100	0.17635	0.17368	0.22767	RANDOM	17.071

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	36.075
r_dihedral_angle_4_deg	18.644
r_dihedral_angle_3_deg	15.742
r_dihedral_angle_1_deg	6.608
r_scangle_it	4.043
r_scbond_it	2.644
r_angle_refined_deg	1.806
r_mcangle_it	1.611
r_mcbond_it	0.957
r_chiral_restr	0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.075
r_dihedral_angle_4_deg	18.644
r_dihedral_angle_3_deg	15.742
r_dihedral_angle_1_deg	6.608
r_scangle_it	4.043
r_scbond_it	2.644
r_angle_refined_deg	1.806
r_mcangle_it	1.611
r_mcbond_it	0.957
r_chiral_restr	0.134
r_bond_refined_d	0.017
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3799
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	20

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 R01GM157729.