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Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase
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 8.5 294 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.23 α = 90 b = 95.4 β = 119.98 c = 91.2 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 2013-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.982 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.68 19.35 98 0.09 12.1 2.8 151200 151200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.78 93.6 3.7 2.4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4R2X 1.68 19.35 143534 7639 98.21 0.13918 0.13797 0.16142 0.1451 RANDOM 14.952
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] -2.43 -1.42 14.48 -12.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.712 r_dihedral_angle_4_deg 16.085 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 6.901 r_long_range_B_refined 3.357 r_long_range_B_other 3.245 r_scangle_other 2.029 r_angle_refined_deg 1.957 r_mcangle_it 1.762 r_mcangle_other 1.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.712 r_dihedral_angle_4_deg 16.085 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 6.901 r_long_range_B_refined 3.357 r_long_range_B_other 3.245 r_scangle_other 2.029 r_angle_refined_deg 1.957 r_mcangle_it 1.762 r_mcangle_other 1.762 r_scbond_it 1.37 r_scbond_other 1.368 r_mcbond_it 1.197 r_mcbond_other 1.197 r_angle_other_deg 1.032 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10886 Nucleic Acid Atoms Solvent Atoms 841 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing