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Staphylococcus aureus superoxide dismutase SodM double mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 30 mM MgCl2, 30 mM CaCl2, 39.1 mM Bicine, 60.9 mM Trizma pH 8.5, 20 % PEG 550 MME and 10 % PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.21 61.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.21 α = 90 b = 144.21 β = 90 c = 49.22 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 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 0.976 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 1.5 47.2 100 0.999 18.6 11 93785
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 1.5 1.53 100 0.659 1.9 11.2
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 6EX4 1.5 47.2 94477 5090 99.96 0.14013 0.13844 0.1476 0.1719 0.1503 RANDOM 29.266
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] 1.74 0.87 1.74 -5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.04 r_dihedral_angle_4_deg 25.487 r_dihedral_angle_3_deg 12.661 r_dihedral_angle_1_deg 6.274 r_scangle_other 5.262 r_long_range_B_refined 4.782 r_long_range_B_other 4.723 r_scbond_it 4.679 r_scbond_other 4.679 r_rigid_bond_restr 4.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.04 r_dihedral_angle_4_deg 25.487 r_dihedral_angle_3_deg 12.661 r_dihedral_angle_1_deg 6.274 r_scangle_other 5.262 r_long_range_B_refined 4.782 r_long_range_B_other 4.723 r_scbond_it 4.679 r_scbond_other 4.679 r_rigid_bond_restr 4.162 r_mcangle_it 3.235 r_mcangle_other 3.235 r_mcbond_it 2.732 r_mcbond_other 2.724 r_angle_refined_deg 1.655 r_angle_other_deg 1.569 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3230 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 2
Software Software Software Name Purpose GDA data collection xia2 data reduction XDS data reduction XDS data scaling Aimless data scaling MOLREP phasing Coot model building REFMAC refinement