That is going to be rough for a puppy. I've worked nights and my dogs adjusted fine to the schedule, but they were all adults by then.
Perhaps keep her up later? Is she going to sleep in the evening and then well rested by 5am? Try keeping her up, exercise her very late and see if that helps at all. Might also help to get up and take her for a potty break, then put her in an xpen rather than back in the crate with some toys, a peanut butter kong, a kong treat ball - anything safe to occupy her for a little longer,.