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Crystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in complex with 2'-Deoxyguanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G2O
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
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1755 0.24894 0.2487 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