Fig. 4: PDB wide analysis on mismodeled helices.
From: Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations
a Structural analysis performed on 1395 deposited cryo-EM structures from the Protein Data Bank, with resolution <6 Å. The structures have been analysed to predict base pairings that are not present in the deposited PDB, but that could exist based on the sequence. The total number of unpaired nucleotides was then divided by the length of the sequence (the values range from 0 when all the base pairings are formed, to 1 if no base pairs exist). The blue data points represent RNA-only structures, while the pink ones are RNA-protein complexes. The group II intron ribozyme investigated here (6ME0) is highlighted in green and examples of PDBs where many unformed base pairs are found (7MSM, 7OLC, 7UIN, 8E35) are marked with Xs. Source data are provided as a Source Data file. b Examples of mis-modeled base parings, in more pathological cases (7MSM) and less serious ones (8E35), taken from the aforementioned PDBs.
