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Mutant D24G of uridine phosphorylase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Potassium sulfate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.02 39.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.1 α = 90 b = 150.1 β = 90 c = 50.06 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 DECTRIS PILATUS 6M 2018-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9537 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 30 97.2 0.89 11.1 2.6 41245
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 0.67
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4R2X 1.75 30 41244 2187 97.216 0.166 0.163 0.1644 0.2185 0.2185 29.153
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] -0.403 -0.202 -0.403 1.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 20.07 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 7.012 r_lrange_it 6.218 r_scangle_it 5.99 r_scbond_it 4.744 r_mcangle_it 3.524 r_mcbond_it 3.005 r_angle_refined_deg 2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 20.07 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 7.012 r_lrange_it 6.218 r_scangle_it 5.99 r_scbond_it 4.744 r_mcangle_it 3.524 r_mcbond_it 3.005 r_angle_refined_deg 2.226 r_nbtor_refined 0.315 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.181 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.134 r_metal_ion_refined 0.052 r_bond_refined_d 0.015 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3752 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing