Dear Bert, Your density reminded me a little bit of the paper by Pearson et al. Biochemistry 39:8575-8584(2000) which describes the water structure in the catalytic center of urease. I just went back to it and it looks like Figure 3 in that paper may hint some similarities to your case, in that you may indeed have a mixture of water models.
You did not say if your data comes from cryo-cooled crystals that were manipulated in similar or different ways, or whether one of the two is a room temperature data set. One of the largely overlooked issues related to crystal cryo-cooling concerns the structure attained by the solvent. Structures of urease at 100K and 298K (pdb entries 1ejw and 1ejx) show marked differences in the water structure in the active site and elsewhere. This phenomenon has been observed in other structures as well, and not just with respect to water structure but also for loops and side-chains. Even two cryo-cooled crystals that are manipulated in similar ways may exhibit differences. Bart Hazes addressed some of these issues in an interesting paper in Acta Cryst. (2005). D61, 80-87. Nonetheless, to maximize the chances for the best interpretation possible I would first improve phase accuracy by completing the solvent model as much as possible (except from the contested density), and then use post-refinement residual Fo-Fc density to evaluate possible water models (and other possible interpretations) for the density in question. Best wishes Savvas ----- Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 http://www.lprobe.ugent.be/xray.html -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Van Den Berg, Bert Sent: Tuesday, July 07, 2009 10:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unknown density Dear all, I have attached a jpeg of some (2fo-fc) density in the active site of a protein I'm refining (1.9 A data, Rfree 24%, still need to pick waters etc; oxygen atom placed in the approximate center for reference). It looks like there are 3 non-hydrogen atoms sandwiched between an Asp, His and Arg. The molecule seems hydrogen bonded to all these three residues. Has anybody any idea what this can be? In a map of another crystal of the same crystal form at lower res (2.3 A), there is a clear, single water molecule between the Asp and His. Are they waters at partial occupancies (there is not enough room for 3 separate waters)? The only other thing I can come up with is formate, but that wasn't used in the crystallization. Any hints appreciated! Thanks, Bert Bert van den Berg UMass Medical School Worcester, MA 01605 E-mail message checked by Spyware Doctor (6.0.1.441) Database version: 6.12770 http://www.pctools.com/en/spyware-doctor-antivirus/
