view article
Figure 4
Tomogram alignment quality assessed by AreTomo3 for minicells of Mycoplasma mycoides JCVI-Syn3A acquired with and without a Volta phase plate (VPP). (a) Example tomographic slices illustrating AreTomo3-measured tilt-axis orientation. In the left example, the measured tilt axis (red) closely matches the calibrated instrument tilt axis (yellow, −96.06°). In the right example, the measured axis deviates substantially from the calibrated value, indicating poor global alignment. (b) Tilt-series images non-VPP (left) and VPP (right), annotated with AreTomo3-measured local shifts. The non-VPP example contains a problematic local shift flagged by AreTomo3 (red box), whereas the VPP example shows no such issues. (c) Distributions of measured tilt-axis orientations for VPP and non-VPP tomograms. The VPP dataset exhibits a smaller standard deviation, indicating more consistent tilt-axis determination. (d) Distributions of problematic local alignment fractions for VPP and non-VPP datasets. A larger fraction of VPP tomograms (61%) show zero problematic local shifts, compared with 42% for non-VPP tomograms. (e) Comparison of AreTomo3-measured thickness for VPP and non-VPP datasets, which indicates that the specimen-thickness distributions are comparable between the two datasets.

IUCrJ
Volume 13| Part 3| May 2026| Pages 260-272
ISSN: 2052-2525
https://doi.org/10.1107/S2052252526002575