Don't laugh...but a good way to get doggie mess odours from lingering on your hands & arms after cleaning them up, is to wash yourself with toothpaste.

So it could be worth using toothpaste to clean the crate. Buy the cheapest brand you can find because the basic ingredients are much the same. Then you can be generous in how much you use.

There's also special products to be found in supermarkets among the room deodorant spray products. They aim at neutralizing odours...not just spraying 'nice smells' over the top of 'bad smells'. One has a brand name 'Nil Odour'...others have written on the can that they neutralize smells. Look for the ones that include cleaning up pet messes on the directions on the can. These neutralizing products cost more than the regular room sprays.

I'd thoroughly wash the crate with toothpaste first. Then when it's dry, spray it with one of the 'bad smell' neutralizers which are suitable for pet messes.
Marie