You bought a new system with what on it if anything for a preinstalled OS? If the drive was already partitioned, formatted, and included an operating system namely Windows there will be a hidden recovery partition storing files, drivers there. If you installed Windows onto a bare drive then you created a primary that was simply smaller then the actual drive space available.
On new 500gb drives here the total amount of space available following partitioning was about 465gb. It sounds like one of the two things happened there. Was there an OS already installed on the drive?