☰ Navigation Tabs
X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution
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 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.255 α = 71.81 b = 73.11 β = 77.19 c = 83.137 γ = 85.69
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 2015-05-16 M SINGLE WAVELENGTH
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 2.243 77.231 91.1 0.055 0.077 0.055 9.6 1.7 58293 58293
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 2.243 2.36 83.2 0.333 0.333 0.333 2.3 1.7 7810
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 THROUGHOUT 4LWZ 2.243 45.47 55318 2849 90.88 0.1716 0.1683 0.1686 0.237 0.2367 RANDOM 30.999
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] -0.05 -0.04 0.08 -0.17 0.01 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.205 r_dihedral_angle_4_deg 19.146 r_dihedral_angle_3_deg 15.511 r_dihedral_angle_1_deg 6.204 r_mcangle_it 2.539 r_scbond_it 1.872 r_mcbond_it 1.546 r_angle_refined_deg 1.532 r_chiral_restr 0.118 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.205 r_dihedral_angle_4_deg 19.146 r_dihedral_angle_3_deg 15.511 r_dihedral_angle_1_deg 6.204 r_mcangle_it 2.539 r_scbond_it 1.872 r_mcbond_it 1.546 r_angle_refined_deg 1.532 r_chiral_restr 0.118 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11263 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 167
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction