We refine two low-order structure factors of the skutterudite CoSb3 using convergent beam electron diffraction. The relatively large unit cell of this material causes the disks to overlap and introduces a series of challenges in the refinement procedure. These challenges and future work-arounds are discussed. The refined structure factors F200 and F600 are compared to X-ray diffraction and density functional calculated values, the latter calculated using two different functionals. Both relaxed and experimental lattice parameters are tested to explicitly highlight the impact of the lattice geometry and atomic position on the structure factors.