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Crystal structure of monomeric Cu/Zn-superoxide dismutase in complex with de novo designed binder (#313-604)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold The starting model was predicted using a modified AlphaFold2 protocol with an externally provided initial structural guess, following the AF2 initial guess method (Bennett et al., 2023).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1M zinc acetate, 16% (w/v) PEG 8000, 0.1M MES pH 6.5, 15% trehalose
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.227 α = 90 b = 88.545 β = 90 c = 186.871 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 EIGER X 16M 2025-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 46.72 99.47 0.134 0.041 0.999 14.56 11.9 17976 70.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 99.55 2.38 0.708 0.732 1.29 12
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 2.7 46.72 17067 893 99.72 0.2934 0.29063 0.2847 0.3439 0.3371 RANDOM 94.587
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] -10.24 -5.42 15.66
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.209 r_long_range_B_other 22.209 r_dihedral_angle_3_deg 14.647 r_scangle_other 14.238 r_mcangle_other 14.136 r_mcangle_it 14.114 r_dihedral_angle_2_deg 12.211 r_scbond_it 9.322 r_scbond_other 9.315 r_mcbond_it 9.2
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.209 r_long_range_B_other 22.209 r_dihedral_angle_3_deg 14.647 r_scangle_other 14.238 r_mcangle_other 14.136 r_mcangle_it 14.114 r_dihedral_angle_2_deg 12.211 r_scbond_it 9.322 r_scbond_other 9.315 r_mcbond_it 9.2 r_mcbond_other 9.071 r_dihedral_angle_1_deg 5.549 r_angle_refined_deg 1.275 r_angle_other_deg 0.44 r_chiral_restr 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 2877 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing Coot model building REFMAC refinement