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Crystal structure of E40K variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris) in the apo form complexed with 22E1 Fv-clasp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 7WX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 2% (v/v) polyethylene glycol 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.04 59.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.616 α = 90 b = 83.601 β = 94.52 c = 185.75 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2023-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.29 47.83 99 0.055 1 7.8 3.4 38902
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.29 3.42 0.847 0.59 0.8
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 3.29 43.94 36984 1918 98.98 0.27938 0.2769 0.2723 0.32642 0.3156 RANDOM 149.494
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] 20.31 4.14 -2.89 -17.85
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 28.717 r_long_range_B_other 28.717 r_scangle_other 21.159 r_mcangle_it 19.666 r_mcangle_other 19.665 r_dihedral_angle_3_deg 15.086 r_scbond_it 13.19 r_scbond_other 13.189 r_mcbond_it 12.534 r_mcbond_other 12.534
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 28.717 r_long_range_B_other 28.717 r_scangle_other 21.159 r_mcangle_it 19.666 r_mcangle_other 19.665 r_dihedral_angle_3_deg 15.086 r_scbond_it 13.19 r_scbond_other 13.189 r_mcbond_it 12.534 r_mcbond_other 12.534 r_dihedral_angle_1_deg 6.767 r_dihedral_angle_2_deg 6.123 r_angle_refined_deg 0.978 r_angle_other_deg 0.35 r_chiral_restr 0.044 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 12453 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing Coot model building XDS data reduction