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Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121E
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 6.5 293 sodium fluoride, sodium bromide, sodium iodide, imidazole, MES, PEG MME 500, PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.765 α = 90 b = 113.174 β = 90 c = 119.908 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 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) Rpim 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 1.4 46.52 99.3 0.079 0.085 0.033 0.998 13.5 6.7 195703
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 98.2 1.002 1.085 0.413 0.783 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5x2j 1.4 44.94 186025 9581 99.23 0.1787 0.1779 0.1937 0.1985 RANDOM 16.885
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] -0.59 -2.93 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_dihedral_angle_4_deg 15.681 r_dihedral_angle_3_deg 12.078 r_dihedral_angle_1_deg 6.831 r_angle_other_deg 1.457 r_angle_refined_deg 1.288 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_dihedral_angle_4_deg 15.681 r_dihedral_angle_3_deg 12.078 r_dihedral_angle_1_deg 6.831 r_angle_other_deg 1.457 r_angle_refined_deg 1.288 r_chiral_restr 0.07 r_bond_refined_d 0.005 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 6468 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms 34
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing