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Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 DL-malic acid, PEG3350
Crystal Properties Matthews coefficient Solvent content 4.22 70.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.92 α = 90 b = 135.82 β = 102.74 c = 76.38 γ = 90
Symmetry Space Group C 1 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 PILATUS3 S 6M 2021-06-05 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) 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 2.8 47.81 96.9 0.107 0.123 0.993 10.19 4.1 37308 51.755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 99.7 0.618 0.706 0.82 2.33 4.338
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 47.81 35445 1863 96.98 0.2361 0.234 0.2365 0.2761 0.2746 RANDOM 55.533
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] -0.04 -0.09 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_3_deg 18.744 r_dihedral_angle_4_deg 13.397 r_dihedral_angle_1_deg 6.382 r_angle_other_deg 1.111 r_angle_refined_deg 1.092 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_3_deg 18.744 r_dihedral_angle_4_deg 13.397 r_dihedral_angle_1_deg 6.382 r_angle_other_deg 1.111 r_angle_refined_deg 1.092 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6380 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing