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Mutant T91A 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 PEG 8000, 1 M lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.66 α = 90 b = 91.66 β = 90 c = 47.56 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 2016-05-27 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 1.9 30 99.4 1 15.6 6.38 35104
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 1.9 2.02 0.87
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 1.901 26.474 35104 1696 99.801 0.159 0.1565 0.1589 0.2108 0.2123 25.321
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] -1.258 -0.629 -1.258 4.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.132 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_3_deg 15.936 r_lrange_it 8.277 r_dihedral_angle_1_deg 7.13 r_scangle_it 7.075 r_scbond_it 5.253 r_mcangle_it 4.013 r_mcbond_it 3.024 r_angle_refined_deg 2.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.132 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_3_deg 15.936 r_lrange_it 8.277 r_dihedral_angle_1_deg 7.13 r_scangle_it 7.075 r_scbond_it 5.253 r_mcangle_it 4.013 r_mcbond_it 3.024 r_angle_refined_deg 2.425 r_symmetry_nbd_refined 0.352 r_nbtor_refined 0.321 r_nbd_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.209 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.157 r_bond_refined_d 0.016 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3575 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing