Sophie does not decipher the code A-P-P-L-E--Langdon does this when they are at Newton's tomb confronted by Teabing.  Sophie's skills come in handy when they are at the bank in Zurich trying to open Sauniere's safety deposit box.  They only have one chance to punch in the right code to get the box from the bank--failure to do this sets off an alarm and bars access to the box.  Robert wants to punch in a set of numbers that they found previously, but Sophie is hesitant.  She claims that the numbers must be reordered; she then punches in the Fibonnaci sequence in the correct order, and the safety deposit box is delivered.