Elefant includes a backup command in the command line utility. To back up your entire site, including the database, to a backups folder in your home folder, use the following commands:
$ cd /path/to/your/site
$ ./elefant backup ~/backups/
This will generate a timestamped backup file, for example backup-2011-12-15-08-23-55.tar.gz. The database backup can be found in the file dump.sql in the backup archive.
Here's an example crontab configuration for nightly backups at 2am:
0 2 * * * cd /path/to/your/site; ./elefant backup ~/backups/