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Staphylococcus aureus superoxide dismutase SodA double mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM MgCl2, 100 mM Bis-Tris pH 5.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.25 α = 90 b = 68.15 β = 100.58 c = 57.29 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 PIXEL DECTRIS PILATUS 6M 2018-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.550 Diamond I03
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 1.8 43.46 99.4 0.995 10.9 6 36588
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 1.8 1.84 96.4 0.73 2.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EX3 1.8 35.77 34541 1735 98.87 0.17252 0.17076 0.1784 0.20685 0.2136 RANDOM 21.466
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] 0.47 -1.65 -0.73 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.038 r_dihedral_angle_3_deg 12.706 r_dihedral_angle_4_deg 6.422 r_dihedral_angle_1_deg 6.259 r_long_range_B_refined 5.963 r_long_range_B_other 5.961 r_scangle_other 5.232 r_scbond_it 3.249 r_scbond_other 3.248 r_mcangle_it 2.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.038 r_dihedral_angle_3_deg 12.706 r_dihedral_angle_4_deg 6.422 r_dihedral_angle_1_deg 6.259 r_long_range_B_refined 5.963 r_long_range_B_other 5.961 r_scangle_other 5.232 r_scbond_it 3.249 r_scbond_other 3.248 r_mcangle_it 2.843 r_mcangle_other 2.842 r_mcbond_it 1.92 r_mcbond_other 1.915 r_angle_refined_deg 1.559 r_angle_other_deg 1.475 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 3198 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 2
Software Software Software Name Purpose GDA data collection xia2 data reduction XDS data scaling Aimless data scaling MOLREP phasing Coot model building REFMAC refinement