[3dem] Membrane protein structure: orientation issue

[Saumya Verma Bajaj]

Dear all,



I am trying to solve the structure of a tetrameric membrane protein
complex, with the protein embedded in detergent micelle (0.05% GDN) and a
soluble accessory protein attached to it.



Following 2D classification, while the side views and oblique views are
easily visible, and the top/bottom are very few (~1-2%) (please see
attached image) and get further diminished in subsequent rounds of 2D
classification.



While we are trying different grid types to overcome the orientation
problem at the sample level, I was wondering if there are certain tweaks we
can make to the analysis parameters (particle picking, box size, mask, ctf
etc.) to enhance the signal of protein embedded within a micelle in the
current data set. We are using Relion3.1 for SPA.



Any suggestions to salvage this set of data will be very helpful.



Thank you.

Best regards,

Saumya
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200325/3d4a7d9e/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2Dclasses.png
Type: image/png
Size: 618877 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200325/3d4a7d9e/attachment-0001.png>