I’m skeptical that the oil is acting as a reservoir for the metal, as shouldn’t the metal be too hydrophilic to partition into the oil phase? This is testable, at least.
Another (to me, more plausible) explanation is that there are subtle differences in water activity in your two crystallization setups. Many years ago (doi: 10.1021/bi00013a021) I saw a metal change position owing to crystal dehydration and concomitant subtle shifts in atomic positions; perhaps this is what’s going on? FWIW, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu > On Apr 22, 2025, at 5:03 AM, Flavio Di Pisa <dipi...@gmail.com> wrote: > > Dear community, > I’ve observed differences when crystallizing the same protein using two > different setups: microbatch under (Al’s) oil and vapor diffusion sitting > drop. > The protein crystallizes in a condition containing 50 mM cadmium as one of > the precipitating agents. In the sitting drop setup, I observe 2 well-defined > cadmium ions at the so-called mineralization site (please see PDB entry 5lg8 > and the related paper: https://www.pnas.org/doi/10.1073/pnas.1614302114), > with occupancies close to 1, as confirmed by the anomalous signal, plus other > "anomalous blob" near to this site. > However, in the microbatch under oil setup, I never observe these cadmium > ions. Instead, I consistently detect only one cadmium ion with high > occupancy, and occasionally a second one with lower occupancy. > In summary, crystallizing the same protein using these two setups results in > different metal-binding behavior. > My question is: could it be that in microbatch under oil, ions might diffuse > away from the mineralization site? Could this account for the reduced number > of cadmium ions observed? Additionally, and more importantly, could the > crystallization setup influence the soaking efficiency of other metals, such > as iron (the natural substrate of this protein)? > I’ve attached two screenshots: > • One (orange blob) represents the protein crystallized via vapor > diffusion, showing two well-defined anomalous peaks. > • The other shows the same site in a crystal grown via microbatch, where > only one anomalous signal (in white) is visible. > I hope I’ve been clear. Thank you in advance, and I wish you all a great day! > Best regards, > Flavio > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <Schermata > del 2025-04-22 10-54-23.png><Schermata del 2025-04-22 10-54-51.png> Patrick Loll pjl...@gmail.com ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
