FWIW, the steep angle of those crater walls is almost purely a function of the "angle of repose" -- characteristic of that particular soil.
Like you, I am surprised at the depth of the crater. I wonder if the explosives-filled car could have been of the "gondola" or bottom-dumping -- type. That could have vented more of the explosion downward...
However, the aboveground part of the blast did extend for an awfully long way:
That explosion had a much more extended destructive range than did the explosion of about a traincar-load of ammonium nitrate at West, Texas, a few years ago. And the West crater was almost negligible in depth...
BTW, do you know where the scientists supposedly were when they were kiled? In a passing train on the main line?
Anyone close enough to time the explosion to hit a specific passing train car would have been dangerously close -- even with a cell phone-controlled initiator.
Is there a possibility that the explosion could have taken out the super-spy, as well?