Preflop
3 BB open is pretty standard for cash games these days and totally fine.
Flop
I love the fact, you raised his donk bet rather than getting into a silly slowplay mode. Yes you block top pair, but he can be donking a lot of draws, and you are 200BB deep, so make him pay to see the next card. You went for around 75% pot, which I think is fine, but given how much stack was left behind, and the fact you had the stone cold nuts, this is certainly a spot, where you could explore some even bigger bet sizes against a presumably recreational opponent. Make it a dollar to go, and he will probably still pay with the same range of hands. Classic "crushing the micro stakes" situation.
Turn
Not the greatest turn, since it did make a bunch of different gutshots come in, and a lot of hands picked out equity with 16 cards in the deck now putting out a 1-liner on the river. I am still on board with betting for value though, but now I prefer a slightly smaller size like 60-70% pot. Its rather backward, that you size up, when the relative strenght of your hand just got a lot worse.
And then of course the interesting part is, when he check-jam. This is pretty gross, but I agree with the other guys, that its difficult to fold top set here, when the hands, that made a straight, were only gutshots on the flop. With 100BB stacks it would be a snap call, but for 200BB it is really gross. I would probably still pay him off though thinking, that maybe he is panicking about the wet board and doing this "for value" with a worse set or two pair.
Conclusion
Classic bad beat in the micro stakes, and as explained in this video there is nothing, you can really do about it. Other than perhaps make him pay even more to chase after that 4-outer on the flop. Not that he would nessesarely have folded, but then at least you win more all those times, where he dont nail his card.
https://www.youtube.com/watch?v=iK7kK-p_c6A