Best is an orthogonal process (like NMR). Cryo-EM is getting better too so maybe that will start to be viable. Sometimes that's not possible, but you can use

Best is an orthogonal process (like NMR). Cryo-EM is getting better too so maybe that will start to be viable. Sometimes that's not possible, but you can use secondary evidence: "we know these three amino acids are important band hey look they touch in our model".