☰ Navigation Tabs
X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O
Crystal Properties Matthews coefficient Solvent content 2.25 45.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.258 α = 69.35 b = 71.772 β = 72.17 c = 89.228 γ = 85.78
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 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.00 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.109 46.083 89.2 0.039 0.999 15.59 3.3 501694 -3 9.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.109 1.18 69.8 0.405 0.839 2.34
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 4K6O 1.109 39.675 1.91 501489 5265 89.22 0.1145 0.1143 0.1155 0.1359 0.1367
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 20.77 f_angle_d 1.401 f_chiral_restr 0.107 f_bond_d 0.014 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11301 Nucleic Acid Atoms Solvent Atoms 1508 Heterogen Atoms 220
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction