If it were mine, I would probably fill it to about one-third with small colored glass pebbles of a single color or mixed; maybe the clear iridescent ones, with a few of the pale blue and pale green ones mixed in.
I love malachite too, but I don’t think that choice in this application would compliment either the jar or the stones very well. I have a small arrangement of single polished malachite chunks, each worthy of admiration in its own right. I think a large quantity of them would detract from one another and not set off the vase so well either. Something that lets light pass through seems most attractive to me.
@gailcalled, I’ve done the same thing with beautiful (but empty, alas) perfume bottles.