Can Isopropyl β-D-1-thiogalactopyranoside be degraded into either 1-deoxy-galactose or just galactose? This may be a silly question, but is it feasible that Isopropyl β-D-1-thiogalactopyranoside (IPTG) when acted upon by a beta-galactosidase could produce 1-deoxy-galactose or just galactose?

The reason I am asking is because I have a crystal of a beta-galactosidase that was exposed to 5mM IPTG for ~6 months at 4 degrees C for inhibitor studies.I have X-ray crystallographic data (Beta-galactosidase + IPTG) to ~1.8 angstroms and can easily place the galactosyl ring into my electron density, however, I cannot place the sulfur atom or the isopropyl group.

This would normally indicate that the sulfur and isopropyl atoms are disordered, however, the possible conformations are sterically restricted to one direction.

As such I am wondering if IPTG could, in fact, have been turned into either 1-deoxy galactose or galactose?
I'm not sure if I understood your question correctly, and my thought is based on this assumed reaction:

Your indication of a resolution of about 1.8 Å reads like the data were collected by Cu K$\alpha$ radiation, rather than by Mo K$\alpha$.  If sulfur was split off from your molecule, than (even more with softer Cu than Mo X-rays) this should have decreased a lot the contribution of anomalous scattering in the X-ray data, as CHO's atomic scattering factors -- in comparsion -- are mainly described by $f'$, and not so much about $f''$. What about looking on value .and. esd of the Flack parameter of your model for your new product, compared to a &quot;typical / reference&quot; model of IPTG?
(By the way, Howard Flack passed away just at the beginning of this year.)