The Pure Crystal is an unused item. Its intended origin is unknown, but its item description suggests it may have been a Shadow Crystal purified by Seam.
Unlike other cut items, the Pure Crystal has a use in the final version of the game: along with the Thorn Ring, it is used to craft the Twisted Sword. However, because the Pure Crystal is currently unobtainable in-game, the Twisted Sword cannot be crafted.