2.6.  Model building  
The atomic interpretation of the SARS-Cov-2 spike 3D map (PDB entry 6zow) was performed taking advantage of the modeling tools integrated in Scipion as described in Martínez et al. (2020 ▸). Owing to a lack of sufficient density for the ‘up’ conformation of the RBD, we rigidly fitted the structure of chain A (residues 336–525) of the SARS-CoV-2 RBD in complex with CR30022 Fab (PDB entry 6yla; J. Huo, Y. Zhao, J. Ren, D. Zhou, H. M. Ginn, E. E. Fry, R. Owens & D. I. Stuart, unpublished work) to the 3D map using UCSF Chimera (Pettersen et al., 2004 ▸). This unmodeled part of the structure was called chain ‘a’ since it was part of chain A in the structure previously inferred from the same data set (PDB entry 6vsb; Wrapp et al., 2020 ▸). The rest of the molecule was modeled using the same original structure (PDB entry 6vsb) as a template, as well as another spike ectodomain structure in the open state (PDB entry 6vyb; Walls et al., 2020 ▸). The former structure (PDB entry 6vsb) was fitted to the new map and refined using Coot (Emsley et al., 2010 ▸) and phenix_real_space_refine (Afonine et al., 2018 ▸). Validation metrics were computed to assess the geometry of the new hybrid model and its correlation with the map using ‘Comprehensive Validation (cryo-EM)’ in Phenix, the EMRinger algorithm (Barad et al., 2015 ▸), Q-score (Pintilie et al., 2020 ▸) and FSC-Q (Ramírez-Aportela, Maluenda et al., 2020 ▸). Score values considering the whole hybrid spike and excluding the unmodeled RBD are detailed in Supplementary Table S1. The hybrid atomic structures were submitted to the PDB.
iMODFIT (Lopéz-Blanco & Chacón, 2013 ▸) was employed to flexibly fit the hybrid atomic structure to the open and closed class maps.