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Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.95 293 Protein was combined with equal volume of well solution comprising 200 mM NaCl, 100 mM BisTris (pH 5.95) and 25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.36 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.311 α = 90 b = 68.311 β = 90 c = 188.025 γ = 90
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 2020-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.3 48.3 99.8 0.211 0.219 0.058 0.995 9.9 14.2 38056 28
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 2.3 2.38 97.7 1.451 1.505 0.396 0.692 14.1
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 5wl2 2.3 48.3 36041 1957 99.75 0.2143 0.2119 0.2167 0.2573 0.2599 RANDOM 32.413
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] -0.53 -0.53 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.791 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_1_deg 18.703 r_dihedral_angle_3_deg 16.382 r_angle_refined_deg 1.661 r_angle_other_deg 1.237 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.791 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_1_deg 18.703 r_dihedral_angle_3_deg 16.382 r_angle_refined_deg 1.661 r_angle_other_deg 1.237 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6080 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction