Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)

Cryo-EM Data Processing
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We’re excited to be sharing a case study on the end-to-end processing of encapsulated ferritin in CryoSPARC! This case study demonstrates some advanced tools and processes that enable processing of a structure with unconventional symmetry and geometry characteristics. Topics covered include:

  • Ab-Initio Reconstruction of high-symmetry datasets
  • handling local symmetry and non-point-group symmetry
  • use of Volume Alignment Tools and Align 3D Maps for custom geometry operations
  • jobs such as 3D Classification, Regroup 3D, Local Refinement, and more

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This dataset consists of an Icosahedral encapsulin nano-compartment enclosing a tetrahedral configuration of four encapsulated ferritin decamers, shown in the figure above. This dataset was collected and originally processed by Jennifer Ross, et al. (2022), and is described in their publication “Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment”. The raw data is publicly available for download as EMPIAR-10716. The case study walks through the processing of both encapsulin and encapsulated ferritin to high resolution.

We hope this detailed guide is a useful resource. If you have suggestions for future case studies or tutorials, please let us know!

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This is excellent, nice work!! Will be very helpful for many folks I’m sure! :blush:

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Thank you so much for preparing this case study! Its very insightful on the use of 3D classification in combination with the Align 3D map jobs.

One question I have: Is there a specific reason you decide to run the final Local refine in section B4 with “Number of extra final passes: 0”, since the default is set at 1? Does it result in overfitting? Just curious if this is something I should strongly consider when running local refine in general.

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Hi @salmen! Michael set this parameter to 0 just to increase the speed of this step. Generally, we expect extra final passes to either improve the map or make no difference.

You could try running with 0 and 1 final passes and comparing to see if you notice any difference, but you do not need to worry about overfitting due to a higher value for this parameter.

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