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Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence glycerol
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 34.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.52 α = 90 b = 150.52 β = 90 c = 46.25 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 2018-04-18 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 1.65 30 97.9 1 7.9 2.24 50485
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 1.65 1.69 0.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4R2X 1.65 30 46523 2353 98.947 0.181 0.1788 0.2293 0.2065 19.565
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] 0.237 0.118 0.237 -0.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_4_deg 22.782 r_dihedral_angle_3_deg 14.63 r_dihedral_angle_1_deg 7.372 r_lrange_it 4.771 r_scangle_it 4.41 r_scbond_it 3.304 r_mcangle_it 2.604 r_angle_refined_deg 2.352 r_mcbond_it 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_4_deg 22.782 r_dihedral_angle_3_deg 14.63 r_dihedral_angle_1_deg 7.372 r_lrange_it 4.771 r_scangle_it 4.41 r_scbond_it 3.304 r_mcangle_it 2.604 r_angle_refined_deg 2.352 r_mcbond_it 2.165 r_nbtor_refined 0.305 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.18 r_chiral_restr 0.147 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.129 r_metal_ion_refined 0.065 r_bond_refined_d 0.018 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3766 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing