Or should I rather use this 360pix one?
It seems like the smallest box where aliasing is a bit less pronounced. A 360pix box may not suffer as much from increased noise (or whatever the cause of decreased resolution was) as the 576pix box. I also have a monomer reconstruction from this same dataset and suspect that it may also suffer from the increased noise. The resolution of that refinement also decreased when increasing the box size though at around 4A, it is difficult to judge how important that is by looking at the maps.
The monomer top view is half the diameter of its side view and only around 60A in the centre of its 256pix box (or 512pix if using the Rosenthal and Henderson equation for choosing a box size). It is also glycosylated at the top and bottom of the monomer so in the 3rd panel from NU refine below, the map is just a tiny blurred spot even in the 256pix box.
256pix box NU refinement of monomer:
512pix box NU refinement of monomer at 1.06apix:
Perhaps I should use a box of 360pix for both the monomer and dimer reconstructions?
For a particle with these characteristics, would it be recommended to do future data collection closer to focus?
It was very difficult to see particles on the micrographs even after applying Topaz denoising which is why we chose higher defocus for the current dataset.