MongoDB Disk Usage with Capped Collections
You have basically allocated space by defining two capped collections, the oplog and the second capped collection in MyDatabase.

Unless you specify the oplogSize, the oplog will be allocated at 5% of free space on the volume containing the MongoDB data (so I am guessing you had ~170GB free).

The second capped collection size would have been defined by you, and then the _id index would be created and grown in addition to the initial allocation as you added data.  The files also contain the data from the other collections, as you mentioned.

The key thing to remember here, is that capped collections pre-allocate the entire amount specified in advance and never grow or shrink.  Besides the indexes that will be added on user defined capped collections (the oplog has no indexes), the capped collection will remain the same size regardless of how much data you put into it, whether that is 500MB or 500TB - think of it as a fixed-size circular buffer. 

If you want to see this in action, try creating another capped collection of, say, 500MB in a different database called foo, you will end up with foo.0 through foo.4 (possibly foo.5 depending on the version) and have 960MB (or 1984MB, again depending on version) of files on disk. That represents the minimum needed to contain a capped collection of that size.