Perhaps in one of the early reported attempts to refine an Hg derivative we did the anisotropic refinement and we reported something of the anisotropy (Hg derivative at a Cu site) in the methods. The quality of the data "allowed" for this (1.9 A resolution, for instance) even though we ended up depositing an isotropic temperature factor only. We thought there was some interest in the "chemistry" of the Hg, and certainly the structure otherwise refined with sensible chemistry (albeit closely related to the Cu chemistry). We achieved a reduction of the two significant peaks with the anisotropic description (along an axis with the Met ligand), not surprisingly perhaps, and ....
...as already stated by Bart: "ripples don't really affect .... the biological conclusions you derive from it", (assuming that there aren't alternative configurations at play). Of course there have been more profound considerations of the Fourier truncation errors in the postings, and wavelength considerations, so effectively all atom and map "behaviour" can be seen to be exacerbated with Hg. I don't recall if we refined occupancy (if we did there was no evidence the Hg was significantly below fully occupied). Cu has been seen to be "knocked out" of some of these copper sites, but this didn't seem to be the situation. Cheers, Bret _______________________________________________________ W. Bret Church Senior Lecturer in Pharmaceutical Chemistry & Group in Biomolecular Structure and Informatics www.sbio.pharm.usyd.edu.au -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of James Holton Sent: Thursday, 2 August 2007 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] difference density ripples around Hg atoms If you are refining against data from near the Hg edge (1.01 A), then you are most likely using an inappropriate scattering factor for Hg. At the edge, as much as 25% of the electrons are "missing" (scattering out of phase). As GMS pointed out, there could also be radiation damage, which means that the Hg atom could be migrating somewhere else (as in Ramagopal 2005), also making the occupancy less than 1.0. You can "soak up" a significant amount of missing electrons with a B-factor, but not completely. B-factors do not change the total number of electrons in the atom, so refining just a B when the "true" occupancy less than 1.0 will match up the peak heights (where the signal is strong) at the expense of the "tails" (where the "signal" is weaker). This will result in a modeled atomic shape that is "too fat", giving you negative ripples in an Fo-Fc map around the atom. I second GMS's suggestion to refine the occupancy. If your refinement program does not have such an option, then you can do it manually: refine a series of models with different Hg occupancies and see which one minimizes the ripples. If that doesn't work, then try anisotropic B refinement. Both radiation damage and anomalous scattering polarization effects can also give ripples around heavy atoms, which you can kinda-sorta model with an anisotropic B. -James Holton MAD Scientist Klemens Wild wrote: > Dear friends of the Fourier transform, > > I am refining a structure with 2 adjacent Hg atoms bound to cysteines > of different monomers in the crystal contacts, which means I need to > refine them as well. While the structure nicely refines (2.2 A data), > I do not get rid of negative density ripple layers next to them (-10 > sigmas). My question: is this likely due to anistropy of the soft > mercury atoms (anisotropic B refinement decreases the ripples) or is > this likely a summation truncation effect prominent for heavy atoms? > Can I just anistropically refine the mercuries while I keep the rest > isotropic? Never saw this in a PDB. Suggestions are very welcome. > > Greetings > > Klemens Wild
