We used 3JBU as our reference structure.
This structure is based on a cryo-electron density map of the Escherichia coli ribosome stalled during translation by the 17 amino acid long arrest peptide SecM (Zhang et al. 2015). It is so-far the best available structure of translational arrest by SecM, which is why we used it for the present study.
While building the model, we noticed that the backbone of the nascent chain contains 4 peptide bonds with the omega dihedral in the cis configuration, which are hard to justify since cis omega dihedrals are rare. Moreover, the cryoEM density of the map in this region is not high enough to justify modelling a cis configuration, and this led us to replace the cis bonds in this region to trans as the first step.
The details of this process can be found in FixCisBonds.
Note: After fixing the cis bonds, we used the same nascent peptide for all our models. The details can be found in Complete70S.