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X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with thymidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 292 0.1 M Bicine, 1.6 M AmSO4
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.919 α = 90 b = 190.919 β = 90 c = 57.718 γ = 90
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 PSI PILATUS 6M 2014-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
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 2.55 39.02 97.39 0.063 15.72 4.5 64691
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 2.55 2.59 94.1 0.761 1.96 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4XR5 2.55 39.019 0.03 64691 3274 97.39 0.1782 0.1762 0.1873 0.2154 0.224 67.7799
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 15.545 f_angle_d 1.325 f_chiral_restr 0.049 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6580 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 146
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing