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Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with pyridin-4-ol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.2 M Ammonium Acetate , 0.1 M Bis-Tris, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.74 α = 90 b = 99.74 β = 90 c = 99.74 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.6 57.585 100 0.114 1 15.1 11.7 43839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 100 0.5 1.5 11.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CXQ 1.6 57.585 1.34 43802 2149 99.98 0.1673 0.1664 0.1857 0.1851
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 f_dihedral_angle_d 13.109 f_angle_d 1.093 f_chiral_restr 0.068 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2148 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement xia2 data reduction XDS data scaling PHENIX phasing Coot model building