Fig. 4: Surface damage analysis of xenon plasma milling using STA.
a Schematic overview of the distance groups and matched controls. The distance of each ribosome to the nearest milling surface was calculated (top), and ribosomes were grouped based on this distance in 5 nm bins (middle). To correct for other factors that affect STA resolution (e.g. local lamella thickness, tilt-series alignment quality), matched controls were created for each distance group by randomly taking the same number of particles from the same tomograms, but further away from the milling surfaces (bottom). b B-factor plots for different 5 nm distance groups from the milling surfaces, up to 60 nm. The 0-5 nm group was excluded from B-factor analysis due to an insufficient number of particles. Resolution is plotted on square inverse scale and particle number is plotted on loge scale, with resolutions reported as mean ± SE (n = 3 technical replicates of the B-factor analysis). c Local resolution maps for one of the n = 3 ribosome structures obtained during the B-factor analysis in b for 800 particles, with the distance group (black) and obtained global resolution (blue) indicated below each map. d Plot of the ratio of mean B-factor for each distance group to its corresponding matched control fitted with a three-parameter exponential decay function (R2 = 0.89). Error bars report SE of the B-factor ratio (derived from n = 3 technical replicates of the B-factor analysis). e Plot of extrapolated difference in resolution (mean ± SE) for 5000 particles between the distance groups and the matched control groups. Exponential decay function fit: y = 22.4e−0.185x + 0.0568 (R2 = 0.98). f B-factor plots for 10,000 particles randomly selected from the sets of: all particles, particles less than 30 nm from the milling surface, particles greater than 30 nm from the milling surface. Linear fit plotted through the linear section of the data. Resolution is plotted on square inverse scale and particle number is plotted on loge scale, with resolutions reported as mean ± SE (n = 3 technical replicates of the B-factor analysis). Source data for all plots are provided as a Source Data File.
