Why is Atticus trying to protect a black man when he was accused of raping a white girl when really it was the white girl's daddy? Also, how did the Judge and Atticus find out that it was the white guy's fault?

Atticus is trying to defend a black man when he was accused of raping a white girl when really it was her dad who did it why is he trying to defend him? I mean, he was killed already so why would he be accused if he didn't do it and the white girl's dad accused Tom? How did they find out that the white guy raped his daughter? According to the book, Tom said he never layed a hand on Mayella, but Bob didn't think so. Why? Please explain clearly!!!!!