Hi Stefan,
I would suggest trying using a larger box size - even at 2x the particle size, you will be cutting off a lot of information for a particle so small.
The box size to use (in order not to lose information delocalized due to the CTF) is:
B=D+(2XLX(dF/D) (from Rosenthal & Henderson JMB 2003)
where D is the diameter of the particle, L is the wavelength (~0.02Å at 300kV), dF is the defocus, and D is the target resolution.
So at let’s say 1.5um defocus with a target res of 5 Å, you would need a box size of 165 Å in this case - and a box size of 90 Å would mean you are losing quite a lot of information beyond 12 Å, if I have it right.
Cheers
Oli