X-ray crystallography has been used to study the structures of some enzymes and their substrates as they undergo catalytic transformation using techniques including flow cells, cryotrapping, temperature jump, pH jump, initiation of reactions by photolysis, time-resolved Laue diffraction. There are nice reviews of the earliest x-ray cryoenzymology work by Makinen and Fink from the 1970's. More recently, look for papers of Ringe and Petsko, Robert Sweet, Ilme Schlichting, Barry Stoddard, Andy Mesecar among others. Generally, evidence that a productive mode of substrate binding is observed comes from the fact that it subsequently undergoes reaction.

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