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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 6W41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.65 293 Protein (9.6 mg/mL) was mixed with an equal volume (2 uL) of well solution comprising 200 mM sodium citrate (pH 6.65) and 24% (w/v) PEG3350. Cryoprotection was achieved by briefly (5-10 sec) swimming crystals in well solution doped with glycerol to a final concentration of ~25% (v/v), prior to snap freezing.
Crystal Properties Matthews coefficient Solvent content 3.27 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.749 α = 90 b = 70.749 β = 90 c = 249.52 γ = 90
Symmetry Space Group P 43 21 2
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 1.69 49.05 99.9 0.075 0.076 0.015 1 26.4 26.6 72750 24.5
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 1.69 1.72 97.7 1.511 1.541 0.298 0.861 25.9
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 6w41 1.69 49.05 68990 3631 99.9 0.1673 0.166 0.1771 0.192 0.2004 RANDOM 29.029
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] 0.81 0.81 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.14 r_dihedral_angle_4_deg 19.49 r_dihedral_angle_3_deg 13.083 r_dihedral_angle_1_deg 7.502 r_angle_refined_deg 1.759 r_angle_other_deg 1.506 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.14 r_dihedral_angle_4_deg 19.49 r_dihedral_angle_3_deg 13.083 r_dihedral_angle_1_deg 7.502 r_angle_refined_deg 1.759 r_angle_other_deg 1.506 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3206 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 38
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction