Defence is a big part of the rating.
So lets consider 2 players, Player A and Player B.
Player A has sensational OD and respectable JS and JR.
Player B has tremendous JS and JR but has mediocre OD.
All other skills are the same.
If you are looking at the box score, then player B is going to probably score a lot more points than player A. Assists, turnovers, rebounds, etc are all going to be similar as the other skills are the same.
However, defence isn't a coloumn. So the player rating takes defence in to account. Player B might score 50 points in the game but perhaps whoever he was defending also got 50 points because Player B has bad defence. So Player B will have a low rating. On the contrary, player A might score 12 points, but because he is such a good defender he only lets his opponent score 8 points. So his rating will be higher.
Make sense? :)