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Staphylococcus aureus Mn-dependent superoxide dismutase SodA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M MgCl2, 30 % PEG 4000, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.275 α = 90 b = 68.356 β = 99.45 c = 56.724 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 PILATUS3 6M 2014-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.881 Diamond I04
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 2.07 43.3 91.6 0.996 9 3.5 21845
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 2.07 2.12 51.7 0.953 1.5 1.6
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 1IDS 2.07 43.3 20774 1070 91.84 0.15415 0.1497 0.1601 0.23888 0.2443 RANDOM 38.482
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] 3.68 0.94 -1.69 -2.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.011 r_dihedral_angle_2_deg 40.111 r_sphericity_bonded 26.596 r_dihedral_angle_3_deg 13.872 r_dihedral_angle_4_deg 9.038 r_dihedral_angle_1_deg 5.885 r_long_range_B_refined 5.86 r_long_range_B_other 5.849 r_mcangle_other 5.329 r_mcangle_it 5.327
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.011 r_dihedral_angle_2_deg 40.111 r_sphericity_bonded 26.596 r_dihedral_angle_3_deg 13.872 r_dihedral_angle_4_deg 9.038 r_dihedral_angle_1_deg 5.885 r_long_range_B_refined 5.86 r_long_range_B_other 5.849 r_mcangle_other 5.329 r_mcangle_it 5.327 r_scangle_other 5.28 r_scbond_it 4.405 r_scbond_other 4.404 r_mcbond_it 4.254 r_mcbond_other 4.252 r_rigid_bond_restr 2.874 r_angle_refined_deg 1.563 r_angle_other_deg 1.018 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3202 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement