CRISPR-Cas9-sgRNA modeling

Protein coordinates were taken from the crystal structure of CRISPR-Cas9 in complex with sgRNA and double stranded DNA (PDB ID 5F9R) [36]. The protein was split up into seven domains (Arg, CTD, HNH, Helical-I, Helical-II, Helical-III, and RuvC) and each was fit individually into the 4.5 Å cryoEM map (EMD 3276) [36]. The protein domains were kept fixed throughout the DRRAFTER run. Ideal A-form RNA helices were fit into the map for all helical sections of the sgRNA. Models were built for sgRNA residues 11–99, but RMSDs were only computed over residues with coordinates in the 2.9 Å crystal structure, PDB 4ZT0 (residues 11–30 and 57–99) [37]. Models were similarly built into the 2.9 Å crystallographic density map (4ZT0), but with the protein coordinates taken from 4ZT0.