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X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LWZ
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 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.949 α = 67.54 b = 76.336 β = 73.74 c = 89.694 γ = 84.92
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 2015-05-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.97989 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.63 45.157 93.2 0.08 0.096 0.053 10.5 3.3 164109 164109
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 1.63 1.72 84.2 0.428 0.428 0.281 1.7 3.2 21679
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LWZ 1.63 19.97 154258 8011 92.16 0.1652 0.163 0.2073 0.1905 RANDOM 20.75
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] -0.16 -0.17 0.04 -0.07 -0.11 0.13
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.684 r_dihedral_angle_2_deg 29.252 r_sphericity_bonded 19.343 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_1_deg 5.427 r_mcangle_it 3.311 r_rigid_bond_restr 3.09 r_scbond_it 3.069 r_mcbond_it 2.515
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.684 r_dihedral_angle_2_deg 29.252 r_sphericity_bonded 19.343 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_1_deg 5.427 r_mcangle_it 3.311 r_rigid_bond_restr 3.09 r_scbond_it 3.069 r_mcbond_it 2.515 r_angle_refined_deg 1.191 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11262 Nucleic Acid Atoms Solvent Atoms 1518 Heterogen Atoms 78
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction