Hi CryoSPARC users! We are excited to share part 2 of our end-to-end processing case study of a nucleosome with a motor protein bound which you can follow along with!
In this extension, we walk through the discovery of an intermediate binding state of ALC1 that was described in Bridges et al. in collaboration with Guillaume Gaullier, Luka Bacic, and Sebastian Deindl.
We take you through how you might approach decision-making when analysing heterogeneous mixtures of low-population states including:
-
Creating a difference map to aid ALC1 mask generation
-
Iterative mask design to improve 3D classification
-
3DVA with a generous solvent mask
-
Local Refinement with a custom fulcrum
Throughout, we consider the influence of stochastic events, and how they affect run-to-run reproducibility by showing the results of replicate runs.
We hope this detailed guide is a useful resource for users old and new! If there are other types of targets, or particular single particle cryo-EM challenges that you would like to see a case study on in the future, let us know!
Although you probably want to look at different datasets by now.