Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction

Ali Punjani; Haowei Zhang; David J. Fleet

With a GPU accelerated implementation of non-uniform refinement implemented in the cryoSPARC software package [22] , we demonstrate improvements in resolution and 3D density map quality for a range of membrane proteins, yielding state-of-the-art reconstructions in all cases. We show results on a small membrane protein-Fab complex in a lipid nanodisc, a small membrane protein with negligible density outside of the lipid bilayer, a medium-sized membrane complex with a large detergent micelle, and a sodium channel with flexible domains. A beta version of the algorithm was previously released in cryoSPARC and has been used in structural studies of several other interesting proteins (see Section 8) . Non-uniform refinement is reliable and automatic, requiring no change in parameters between datasets, and with no reliance on hand-made spatial masks or manual labels.