Put a soft blanket in there, some of her favorite toys, and even a shirt of yours... it smells like you and it sometimes comforts them. It helps if the crate is next to your bed as well, so she can still smell you/hear you/see you. Jennifer said that you shouldn't have the crate next to your bed, that it makes the whining worse... but I have to disagree. I used to keep the crate in my bathroom, where she couldn't see me, and she would howl, bark, whine, even bite and claw at the bars. As soon as I put it next to my bed, the whining went down a LOT. She would whine for about 10 minutes, 20 at the most, but it wasn't all that bad. It wasn't a loud, howling whine. Just a soft wimper. They hate being "away from the pack", so if they are near you they don't feel as alone. If putting her next to your bed doesnt help any, you might have to put her in another room, maybe on the other side of the house or if you have a cool, large garage, you could put her out there. It seems cruel I know, but you need your sleep and as others said, she WILL eventually get used to it.
Smaller crates are also better, they are den animals, wolves and dogs, so they like feeling secure.