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Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with cytosine
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 6.5 291 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM magnesium chloride, 30mM calcium chloride, 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.134 α = 90 b = 99.134 β = 90 c = 99.134 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-F 2015-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.36 49.567 100 0.135 15.9 10.6 69723
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.41 100 1.04 6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CXQ 1.36 49.567 1.34 69526 3378 99.77 0.1754 0.1746 0.1766 0.1916 0.1941 25.4999
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 18.175 f_angle_d 0.872 f_chiral_restr 0.082 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2162 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 20
Software Software Software Name Purpose xia2 data scaling xia2 data reduction PHASER phasing PHENIX refinement PDB_EXTRACT data extraction