Addressing preferred specimen orientation in single-particle cryo-EM through tilting

The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates. We present a strategy for tackling preferred specimen orientation in single-particle cryogenic electron microscopy by employing tilts during data collection. We also describe a tool to quantify the resulting directional resolution using 3D Fourier shell correlation volumes. We applied these methods to determine the structures at near-atomic resolution of the influenza hemagglutinin trimer, which adopts a highly preferred specimen orientation, and of ribosomal biogenesis intermediates, which adopt moderately preferred orientations.