Thanks Daniel!
These are affinity purified and look quite pure by SDS-PAGE and mass photometry, but there’s a chance there are some empty smalps that came along. Conformational variability is also a definite possibility.
One of the things that I’ve noticed in 2D is that for many of the classes the particles seem to get stuck centered on an “edge” of either the lipid or protein portion of the particles (row 1 image 1, row 1 image 8 in 100K particle image). I imagine this is tough since the center of mass for these particles is roughly between the disc and soluble domain, and has little density in the side views I’m capturing. Right now I’m using a ~350 Å box size, I wonder if increasing that would help.