What part of the gold atom causes the small particles to scatter?

In Rutherford’s famous experiment, a beam of alpha particles from a radioactive source was directed at a thin gold foil. An alpha particle has mass and a positive charge, so it will be slowed or deflected when it encounters mass and/or charge. At that time, it was known that atoms contained negatively-charged electrons but were neutral overall. One tentative description for the internal structure of the atom was called the “plum pudding” model. It supposed that an atom was made of positively-charged material with electrons embedded in it, like the fruit in a plum pudding.
Rutherford’s experiment changed all that. Most of the alpha particles went right through the gold foil as if there was no matter there at all! A few were deflected or scattered, some through large angles, suggesting that they had encountered matter of very high charge density. The conclusion from this was that the matter and positive charge of an atom must be concentrated in a very tiny volume so that most of the atom is empty space where there is no matter at all. That tiny volume that contains all of an atom’s positive charge and over 99.9% of its mass is now called the nucleus of the atom.