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Crystal structure of a recombinant hybrid manganese superoxide dismutase from Staphylococcus equorum and Staphylococcus saprophyticus
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 7.5 293 Magnesium chloride, HEPES, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.362 α = 90 b = 57.362 β = 90 c = 105.762 γ = 120
Symmetry Space Group P 32 2 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 2M 2016-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.4 50 100 0.072 0.076 0.025 4.4 9.6 40473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 0.478 0.506 0.162 0.935 9.5
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 1.4 36.21 38397 2025 99.99 0.144 0.1418 0.152 0.1853 0.1929 RANDOM 19.468
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.007 r_dihedral_angle_2_deg 34.727 r_sphericity_bonded 17.592 r_dihedral_angle_3_deg 12.339 r_dihedral_angle_4_deg 6.661 r_dihedral_angle_1_deg 6.102 r_rigid_bond_restr 5.938 r_angle_refined_deg 1.789 r_angle_other_deg 1.096 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.007 r_dihedral_angle_2_deg 34.727 r_sphericity_bonded 17.592 r_dihedral_angle_3_deg 12.339 r_dihedral_angle_4_deg 6.661 r_dihedral_angle_1_deg 6.102 r_rigid_bond_restr 5.938 r_angle_refined_deg 1.789 r_angle_other_deg 1.096 r_chiral_restr 0.134 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1604 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing HKL data reduction HKL data scaling