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?
As for the super-spy, we don't even know how he did it, if he was indeed involved. So we don't even know if he is dead or alive. If somebody knows about it, apparently he is not talking.