How old is your pup? How long have you had her? Was she fully weaned and on solid food before you got her? Are you offering the same puppy food?
She may simply be afraid because this is all new to her. But when in doubt, always get a vet check. Puppies can go downhill REALLY FAST and if there is a medical issue you want to know ASAP. It could be something simple like an ear infection that can be cleared up quickly, or, if left untreated can result in deafness. In addition, she's never been solo before. Mom and the sibs were always there before.
If indeed deaf, you want to learn about teaching visual signals and that she needs to turn and look at you for guidance. A small pen light flashed on the ground can be taught to mean turn and look at me. I've even seen a light used in a simple Morse code for complex signals in Rally competition (WCRL and C-Wags allow handicapped dogs to compete). Special needs can be difficult, especially in the begining, but not at all insurmountable.
As for crate training, this is probably totally new to her, too. The crate should be a safe haven and presented as a fun (or quiet) place to hang out. There are loads of YouTube videos showing crate games. I like to offer super treats for entering and have snuggle toys available in the crate. Keep puppy safety in mind: offer chewable items only when you are around to make sure she doesn't accidentally swallow a choking hazard. The hard part is the with dogs that eat their bedding--and then develop a blockage that requires surgery. You do not need to close the door in the beginning of training. Encourage her to nap in the crate, closing the door for a few minutes at a time and then when opening it up, make sure to treat IN the crate. Look up also "Puppy Culture". It's the best resource for starting a puppy right.
Got some baby pix?