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Based on his observations, Rutherford came up with his own model of the atom. These are two things he knew: (i) atoms have charged subatomic particles: electrons and protons; (ii) the size of these particles was much smaller than the atom itself.

This is because from his own experiments he knew that most of the positive charges go straight through. That is only possible if there are no charged particles in most of the metal sheet.

As shown in the animation, Thomson's model was a sea of positive charge, with a few negative charges spread around. Rutherford's model was that there was mostly empty space, and both positive and negative charges were distributed in this space.