Evaluating the Volta phase plate for improved tomogram alignment in cryo-electron tomography

The Volta phase plate (VPP) can enhance low-frequency phase contrast in cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), but its impact on tomogram alignment has not been systematically assessed. Using sub-2 Å single-particle analysis (SPA) and analytical contrast transfer function (CTF) modeling, we show that despite high-frequency information loss and moderate signal damping, the VPP enhances signal in low-frequency bands that are crucial for tilt-series alignment. We show that VPP tomograms exhibit increased contrast and remain higher in contrast post denoising, for thick and crowded specimens. Quantitative comparison of tomograms acquired with and without the VPP shows improved tilt-axis orientation measurements and a higher fraction of tomograms amenable to local tilt-series alignment. Although acquisition with the VPP yields lower subtomogram averaging (STA) resolution, these results show that the primary benefits of the VPP for cryo-ET are contrast enhancement and improved tilt-series alignment robustness, which are crucial for studying cellular ultrastructure and protein organization in crowded environments, where STA at moderate resolutions remains valuable.