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Crystal structure of isoform 2 of uridine phosphorylase from Schistosoma mansoni in complex with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 16% PEG4000, 20% isopropanol, 100 sodium citrate tribasic pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.83 56.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.53 α = 90 b = 112.53 β = 90 c = 152.351 γ = 120
Symmetry Space Group P 31 2 1
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 225 mm CCD 2009-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.983 97.454 96 0.095 0.107 0.049 9.7 4.5 74612 74612 28.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.09 90.4 0.598 0.598 0.307 1.3 4.6 10159
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 3EUE 1.983 31.77 1.34 74564 3768 95.94 0.1709 0.1689 0.1728 0.2102 0.2117 Random selection
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 13.535 f_angle_d 1.245 f_chiral_restr 0.056 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6594 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction MOSFLM data reduction