Metal crate is an item used in the quest Do No Evil. It is obtained from Ali Morrisane, and should be taken to Ava in order for her to make Ava's alerter. Ava will then hide the crate in the grounds of Draynor Manor, and the player must use Ava's alerter to find the crate in order to test it. Once found, it should be taken back to Ava, who will take it from you, allowing you to use the alerter in the desert.
If you try to open the crate that Ali gives you, it says, "The crate is empty. What? You didn't think Ali Morrisane would give you something for free, did you?"