☰ Navigation Tabs
X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate
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, HANGING DROP 6 290 0.1 M BICINE, 1.6 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.398 α = 90 b = 193.398 β = 90 c = 58.208 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 2015-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.979 BESSY 14.1
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 1.905 136.753 94.9 0.095 0.103 0.04 16.4 6.7 80208 80208 -3 25.28
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 1.905 2.01 99.5 1.207 1.207 0.5 0.6 6.8 12222
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4XR5 1.905 48.29 80103 3856 94.78 0.2018 0.2 0.2006 0.2378 0.2379 Random selection 35.7813
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 16.768 f_angle_d 0.785 f_chiral_restr 0.049 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6581 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 78
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing XDS data reduction