SARS-CoV-2 RBD-Antibody Complex Structural Determination

The complex was concentrated to 10 mg/mL for initial crystal screening by sitting-drop vapor-diffusion in the MCSG Crystallization Suite (Anatrace, MCSG-1, MCSG-2, and MCSG-3) using a NT8 drop setter (Formulatrix). Diffracting crystals were obtained in a mother liquor (ML) containing 0.2 M (NH₄) Citrate, tribasic pH 7.0 and 12% (w/v) PEG 3350. The crystals were cryoprotected by soaking in ML supplemented with 30% (v/v) ethylene glycol. Diffraction data were collected at Advanced Photon Source SBC 19-ID at a 12.662 keV. The data set was processed using XDS^{22 (link)} and data reduction was performed using AIMLESS in CCP4 to a resolution of 2.75 Å. The structure of the complex was solved by molecular replacement using Phaser^{23 (link)} in Phenix^{24 (link)} with a search model of SARS-CoV-2 RBD (PDBid: 6LZG)^{9 (link)} and the Fab structure (PDBid: 5I1E)^{25 (link)} divided into Fv and Fc portions. Remaining model building was completed using COOT^{26 (link)} and refinement was performed in Phenix^{24 (link)}. The data collection and refinement statistics are summarized in Supplementary Table 1. Structural figures were made in PyMol (Schrodinger, LLC).