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Mutant of Superoxide dismutase SodFM1 from CPR Parcubacteria Wolfebacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM sodium chloride, 100 mM sodium acetate pH 5.0 and 20 % w/v polyethylene glycol 6000.
Crystal Properties Matthews coefficient Solvent content 1.97 37.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.49 α = 90 b = 69.71 β = 100.24 c = 58.01 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 2022-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99987 Diamond I24
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 45.79 98.7 0.999 6.5 6.5 43267
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 1.68 0.556 1.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1GV3 1.65 45.79 43245 2167 98.551 0.155 0.1521 0.1521 0.22 0.2201 29.887
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] -1.536 -0.153 3.035 -1.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.742 r_dihedral_angle_3_deg 15.07 r_dihedral_angle_1_deg 6.328 r_dihedral_angle_2_deg 5.633 r_rigid_bond_restr 5.367 r_lrange_it 4.965 r_lrange_other 4.949 r_scangle_it 4.245 r_scangle_other 4.244 r_mcangle_other 3.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.742 r_dihedral_angle_3_deg 15.07 r_dihedral_angle_1_deg 6.328 r_dihedral_angle_2_deg 5.633 r_rigid_bond_restr 5.367 r_lrange_it 4.965 r_lrange_other 4.949 r_scangle_it 4.245 r_scangle_other 4.244 r_mcangle_other 3.584 r_mcangle_it 3.583 r_scbond_it 3.201 r_scbond_other 3.2 r_mcbond_it 2.68 r_mcbond_other 2.653 r_angle_refined_deg 1.659 r_angle_other_deg 0.555 r_symmetry_nbd_refined 0.253 r_nbd_other 0.239 r_nbd_refined 0.233 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_other 0.11 r_ncsr_local_group_1 0.084 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3300 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling Coot model building BUCCANEER model building MolProbity model building PHASER phasing