There are 7 crystals to collect in the game. All 7 are required in Defeat Ganon and All Dungeons goals.
Crystals 5 & 6 are required to purchase the Super Bomb from the Bomb Shop to blow up the side of the Pyramid of Power to access the Pyramid Fairy.
The Crystals goal is to collect all 7 crystals and defeat Ganon. It is only available in Entrance Randomizer.