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Crystal structure of uridine phosphorylase from Schistosoma mansoni in complex with thymine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 200mM ammonium sulphate, 100mM Bis-Tris pH5.5, 20-25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.361 α = 90 b = 84.872 β = 90 c = 87.422 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2011-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9136 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.93 50 97.1 0.106 0.119 10.1 4.7 43916 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.04 88.8 0.59 0.668 2.44
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4TXJ 1.93 42.436 2.01 43896 2195 97.07 0.2163 0.2144 0.2178 0.2519 0.252 Random selection 34.3136
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 11.032 f_angle_d 0.67 f_chiral_restr 0.025 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4252 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 28
Software Software Software Name Purpose XDS data reduction PHASER phasing PDB_EXTRACT data extraction PHENIX refinement GDA data collection XSCALE data scaling