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Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence PEG
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 citrate tribasic monohydrate, 20% w/v Polyethylene glycol
3,350
Crystal Properties Matthews coefficient Solvent content 1.88 34.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.59 α = 90 b = 150.59 β = 90 c = 46.29 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 CCD MAR CCD 165 mm 2018-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.8025 KURCHATOV SNC K4.4
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 1.71 30 99.5 1 9.6 3.82 42058
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 1.71 1.75 0.7
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 1.71 30 42058 2149 99.451 0.208 0.2037 0.2042 0.2808 0.2807 26.903
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] 0.71 0.355 0.71 -2.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.046 r_dihedral_angle_4_deg 19.674 r_dihedral_angle_3_deg 17.174 r_dihedral_angle_1_deg 8.315 r_lrange_it 6.773 r_scangle_it 6.029 r_scbond_it 4.752 r_mcangle_it 4.667 r_mcbond_it 3.893 r_angle_refined_deg 2.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.046 r_dihedral_angle_4_deg 19.674 r_dihedral_angle_3_deg 17.174 r_dihedral_angle_1_deg 8.315 r_lrange_it 6.773 r_scangle_it 6.029 r_scbond_it 4.752 r_mcangle_it 4.667 r_mcbond_it 3.893 r_angle_refined_deg 2.609 r_nbtor_refined 0.315 r_metal_ion_refined 0.234 r_nbd_refined 0.232 r_symmetry_nbd_refined 0.221 r_chiral_restr 0.177 r_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.165 r_gen_planes_refined 0.019 r_bond_refined_d 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3766 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing