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This shipwrecks page says that it was sunk by a new variant of the SM-6 missile. Originally the SM-6 was an anti-air missile. The James sinking included a test of the new variant designed to be used as a very long range anti-surface (anti-ship) missile. BUT the section USS Reuben James (FFG-57)#Final disposition says that the SM-6 test successfully hit and significantly damaged the James, but did NOT sink it. That section claims it took significant further actions by other means (including the use of scuttling charges installed before the test began) I found no references that justify this claim, so I do not know the real story here.
The SM-6 page also claims the missile sank the James.
All three pages (USS Reuben James, SM-6, and shipwrecks of 2016) site the same reference, but it is advertising the success of the missile test and does not specifically say the missile sank the ship.