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Mutant T91S of uridine phosphorylase from Shewanella oneidensis
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 0.1 M Bis-Tris, pH 6.5, 0.2 M ammonium sulfate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.4 α = 90 b = 95.49 β = 120.025 c = 91.41 γ = 90
Symmetry Space Group P 1 21 1
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 2016-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.964 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 25 97 0.99 8.8 5.09 159146
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 1.75 0.88
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 1.654 25 159145 7780 98.289 0.193 0.1909 0.1916 0.2324 0.2338 17.455
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] -18.41 -8.14 32.512 -14.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 18.049 r_dihedral_angle_3_deg 15.799 r_dihedral_angle_1_deg 8.696 r_lrange_it 4.351 r_lrange_other 4.351 r_scangle_it 2.925 r_scangle_other 2.923 r_mcangle_it 2.916 r_mcangle_other 2.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 18.049 r_dihedral_angle_3_deg 15.799 r_dihedral_angle_1_deg 8.696 r_lrange_it 4.351 r_lrange_other 4.351 r_scangle_it 2.925 r_scangle_other 2.923 r_mcangle_it 2.916 r_mcangle_other 2.916 r_angle_refined_deg 2.315 r_scbond_it 2.197 r_scbond_other 2.194 r_mcbond_it 2.179 r_mcbond_other 2.178 r_angle_other_deg 1.537 r_xyhbond_nbd_refined 0.233 r_nbd_other 0.228 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_refined 0.214 r_xyhbond_nbd_other 0.212 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.116 r_symmetry_xyhbond_nbd_other 0.109 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10898 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing