PDB structures were built manually using the program COOT (52). Maps of P68 capsids with imposed icosahedral symmetries were first rotated to the standard 222 orientation (one of the fivefold symmetry axes of the particle in the xy plane is rotated 31.717° from the y axis). The maps were cropped and normalized, the center of the particle was moved to the center of the box, and the map was converted to crystallographic space group P23. The map of the portal and tail with C12 symmetry was cropped, normalized, and interpolated to a crystallographic P6 space group. The high-symmetry space groups were used to reduce the computational resources required for refinement of the structures.

Initially, the structures were built as poly-alanine chains. Noting the positions of residues with large side chains and aligning them to sequences of P68 structural proteins identified individual proteins in the reconstructions. Final models were iteratively refined in real space using the program PHENIX real_space_refine.py and, in reciprocal space in the program REFMAC5, corrected manually in COOT (5254).

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