Fig. 7: Case studies of SARS-CoV-2 RNA polymerase (AlphaFold2 model refinement).
From: Cryo-EM structure and B-factor refinement with ensemble representation
a AlphaFold2 predicted structure, with the colouring indicating the plDDT confidence measure (blue means higher confidence, red means lower confidence), fitted in the deposited map (EMD-30127, grey) b SMOCf plot of the AlphaFold2 (shown in blue) and TEMPy-ReFF refined model (shown in orange). The regions highlighted in grey and pink (correspond to inset regions in Fig. 7d) contain residues that are not present in the deposited model but are present in the AlphaFold2 model and are well-fitted to the map. c Deposited model for the SARS-CoV-2 RNA polymerase (PDB ID: 6M71, blue) fitted in the deposited map (transparent grey). Unassigned regions are visible, at the top and bottom right of the map. d TEMPy-ReFF model (orange) obtained by refining the AlphaFold2 prediction in the deposited map (transparent grey). Newly modelled regions that fit in the density (as in Fig. 6h) are shown with coloured squares.
