Figure 4 |.

Reconstruction resolution and 2D class averages for Topaz particles at decreasing log-likelihood ratio thresholds. (a) Number of particles vs. reconstruction resolution for Topaz particles (increasing number of particles corresponds to decreasing log-likelihood threshold) and randomly sampled subsets of the published particle set. Resolution is as reported by cryoSPARC. For the published particle sets the mean of three replicates is marked with standard deviation shaded in grey. (b) Stacked bar plots show the quantification of the number of true and false positives at each threshold based on 2D class averages. Decreasing threshold corresponds to increasing number of predicted particles. True positives are colored in blue and false positives in orange. (c) 2D class averages obtained at each score threshold for the T20S proteasome (EMPIAR-10025). Number of particles (ptcls) and effective sample size (ess) for each class are reported by cryoSPARC. NaN is reported for classes without any particles assigned. Classes determined to be false positives are marked with orange boxes. Several classes which appear to be false positives at high score thresholds do not contain any particles and, therefore, are not highlighted.