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Staphylococcus aureus triple mutant of superoxide dismutase SodM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 100 mM K thiocyanate, 30% (w/v) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.979 α = 90 b = 58.206 β = 90 c = 128.379 γ = 90
Symmetry Space Group P 21 21 21
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 2014-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 1.75 43.12 100 0.996 9.5 6.8 44670
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 1.75 1.78 99.9 0.882 1.6 7.3
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 2RCV 1.75 43.12 42320 2281 99.93 0.18555 0.18399 0.1937 0.21559 0.2231 RANDOM 25.383
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] 0.22 1.81 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_dihedral_angle_4_deg 27.71 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 5.868 r_long_range_B_refined 4.096 r_long_range_B_other 3.809 r_angle_refined_deg 1.404 r_scangle_other 1.373 r_mcangle_it 0.97 r_angle_other_deg 0.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_dihedral_angle_4_deg 27.71 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 5.868 r_long_range_B_refined 4.096 r_long_range_B_other 3.809 r_angle_refined_deg 1.404 r_scangle_other 1.373 r_mcangle_it 0.97 r_angle_other_deg 0.969 r_mcangle_other 0.969 r_scbond_it 0.86 r_scbond_other 0.86 r_mcbond_it 0.601 r_mcbond_other 0.601 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3234 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 2
Software Software Software Name Purpose GDA data collection XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building