# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
    - CountRef.mrc    gain reference
    - defects.tif     defect map (K3 data only)
    - frames/         unaligned, unbinned multi-frame micrographs
    - mdoc/           MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
    - TS_###.mrc/     
        - TS_###.mrc.st        sorted, motion-corrected tilt series from WARP
        - TS_###.mrc.rawtlt    tilt angle information corresponding to tilt series
        - TS_###.mrc.aln       AreTomo tilt series alignment solution
        - TS_###.mrc.xf        XF file from AreTomo alignment
    - mdoc_edited/             MDOC files with entries for discarded tilts during alignment removed
- tomograms/
    - *.mrc          tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
    - ######.star    combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microscope used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.