It is okay to mix the grammatical number thus in a complex sentence? "Particles" are plural, but they have (based on the available data obtained using electron microscopy) a singular "part" and a singular "envelope":
In the intercellular space and on the surface of about 5% of the cells we detected spherical viral particles 100-120 nm in diameter with an electron-dense internal part and a distinct envelope with "spikes" about 10 nm in length.
Or should one to use a word like each to avoid this number mix-up:
In the intercellular space and on the surface of about 5% of the cells we detected spherical viral particles 100-120 nm in diameter, each with an electron-dense internal part and a distinct envelope with "spikes" about 10 nm in length.