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X-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer compound at 2.13 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O
Crystal Properties Matthews coefficient Solvent content 2.03 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.28 α = 90 b = 91.28 β = 90 c = 137.227 γ = 120
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 2013-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.000039 PETRA III, DESY P11
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 2.13 38.003 100 0.109 0.115 0.036 13.8 9.9 71570 71570 20.22
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 2.13 2.25 100 0.429 0.429 0.146 1.8 9.4 10438
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 4G8J 2.13 19.771 2.12 71255 2155 99.7 0.2101 0.2085 0.2088 0.2619 0.2626 23.23
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 15.044 f_angle_d 1.219 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11063 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction XDS data scaling