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De novo design of binder (#313) to monomeric Cu/Zn-superoxide dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold The starting model was predicted using AlphaFold2 implemented in ColabFold (Mirdita et al., 2022).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.8 293 0.1M magnesium chloride hexahydrate, 28% (w/v) polyethylene glycol 8000, 0.1M Tris pH 8.8
Crystal Properties Matthews coefficient Solvent content 1.67 26.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.415 α = 90 b = 66.061 β = 93.84 c = 69.848 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 2024-07-19 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 1.8 47.94 99.91 0.036 0.036 0.997 13.55 2 28174 26.16
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 1.8 1.86 99.96 0.236 0.236 0.849 2.75 2
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 1.8 47.94 26684 1490 99.92 0.19104 0.18768 0.1972 0.25232 0.2545 RANDOM 31.134
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] -1.41 0.19 0.17 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.042 r_dihedral_angle_2_deg 8.228 r_long_range_B_refined 7.64 r_long_range_B_other 7.638 r_scangle_other 6.224 r_dihedral_angle_1_deg 5.808 r_scbond_it 3.898 r_scbond_other 3.894 r_mcangle_it 3.808 r_mcangle_other 3.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.042 r_dihedral_angle_2_deg 8.228 r_long_range_B_refined 7.64 r_long_range_B_other 7.638 r_scangle_other 6.224 r_dihedral_angle_1_deg 5.808 r_scbond_it 3.898 r_scbond_other 3.894 r_mcangle_it 3.808 r_mcangle_other 3.807 r_mcbond_it 2.59 r_mcbond_other 2.59 r_angle_refined_deg 1.559 r_angle_other_deg 0.511 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 3028 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 5
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUCCANEER model building Coot model building REFMAC refinement