Degassed C-Flat 2/2-3C grids were glow discharged for 30 s at 20 mA. Virus or VLP solution was diluted with 10 nm colloidal gold; 2.5 μl of this mixture was applied to each grid and plunge frozen into liquid ethane using a FEI Vitrobot Mark 2. Grids were stored in liquid nitrogen until imaging.
Tomographic imaging was performed as described previously26 (link). Imaging was performed on a FEI Titan Krios at 300 keV using a Gatan Quantum 967 LS energy filter with a slit width of 20 eV and a Gatan K2xp direct detector. Tomograms were acquired from -60° to 60° with 3° steps using SerialEM27 (link) and a dose-symmetric tilt-scheme28 (link). Images were acquired in super-resolution mode.
Frames were aligned with either the K2Align software, which uses the MotionCorr algorithm29 (link), or with the frame alignment algorithm built into serialEM; frames were aligned and Fourier cropped to 4K x 4K, giving a final pixel size of 1.78 Å/pixel. Defocus for each tilt was determined by CTFFIND430 (link). Tilt images were filtered by cumulative electron dose using the exposure-dependent attenuation function and critical exposure constants described eleswhere26 (link),31 (link). Tilt images were CTF-corrected using ctfphaseflip32 (link) and tomograms were reconstructed using weighted back projection in IMOD33 (link). Tomograms with poor fiducial alignment were discarded (Extended Data Table 1 ). Poor fiducial alignment was defined as alignment residual above 1 pixel in 2x binned data or retaining fewer than 8 fiducial markers. CTF-corrected unbinned tomograms were binned by 2x (3.56 Å/pixel) and 4x (7.12 Å/pixel) with a Lanczos two-lobe anti-aliasing filter.
Detailed dataset parameters are given inExtended Data Table 1 .
Tomographic imaging was performed as described previously26 (link). Imaging was performed on a FEI Titan Krios at 300 keV using a Gatan Quantum 967 LS energy filter with a slit width of 20 eV and a Gatan K2xp direct detector. Tomograms were acquired from -60° to 60° with 3° steps using SerialEM27 (link) and a dose-symmetric tilt-scheme28 (link). Images were acquired in super-resolution mode.
Frames were aligned with either the K2Align software, which uses the MotionCorr algorithm29 (link), or with the frame alignment algorithm built into serialEM; frames were aligned and Fourier cropped to 4K x 4K, giving a final pixel size of 1.78 Å/pixel. Defocus for each tilt was determined by CTFFIND430 (link). Tilt images were filtered by cumulative electron dose using the exposure-dependent attenuation function and critical exposure constants described eleswhere26 (link),31 (link). Tilt images were CTF-corrected using ctfphaseflip32 (link) and tomograms were reconstructed using weighted back projection in IMOD33 (link). Tomograms with poor fiducial alignment were discarded (
Detailed dataset parameters are given in