☰ Navigation Tabs
Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121Y
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 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.926 α = 90 b = 102.624 β = 90 c = 179.017 γ = 90
Symmetry Space Group C 2 2 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 0.98 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 1.51 45.93 99.8 0.105 0.115 0.047 0.997 10.7 6 144687
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 1.51 1.54 99.9 0.789 0.869 0.362 0.792 5.8
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 5x2j 1.51 44.79 137549 7045 99.71 0.1747 0.1714 0.1826 0.2412 0.2471 RANDOM 19.993
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] -0.49 0.38 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.29 r_dihedral_angle_3_deg 13.164 r_dihedral_angle_4_deg 11.71 r_dihedral_angle_1_deg 7.271 r_rigid_bond_restr 5.847 r_angle_other_deg 1.394 r_angle_refined_deg 1.211 r_chiral_restr 0.064 r_bond_other_d 0.007 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.29 r_dihedral_angle_3_deg 13.164 r_dihedral_angle_4_deg 11.71 r_dihedral_angle_1_deg 7.271 r_rigid_bond_restr 5.847 r_angle_other_deg 1.394 r_angle_refined_deg 1.211 r_chiral_restr 0.064 r_bond_other_d 0.007 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6490 Nucleic Acid Atoms Solvent Atoms 1166 Heterogen Atoms 34
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing