Hi Petr, A few thoughts:
1) The Bijvoet difference Fourier is an approximation to the true imaginary part of the electron density, and because of this shifts in the positions of peaks in this map relative to the 2Fo-Fc map might be expected. This is described in Hendrickson et al. Acta Cryst A43 121-125. 2) It might be possible that the responsible anomalous scatterer is not Sr but something else that is lighter (although perhaps not likely given the wavelength the data was collected at). If a heavier atom is incorrectly modeled in place of a lighter one, it can exacerbate the spurious shifts in the BDF peaks. This is discussed in the reference above. I guess the same thing could occur if the site of interest is less than fully occupied but modeled with full occupancy. 3) It might be informative to verify the anomalous scatterer positions with imaginary LLG maps, which can be calculated using Phaser (or SHARP). Philip On Thu, Apr 24, 2014 at 5:39 AM, Petr Leiman <petr.lei...@epfl.ch> wrote: > Dear All, > > We are looking for an explanation for a very strange observation. > > *Problem*: > We have *two fully independent data sets* (two different crystals), in > which the Bijvoet Difference Fourier map peak of one particular metal site > is shifted by 0.47 A from its position in the 2Fo-Fc map. > > *Relevant information*: > The resolution of both data sets is 1.5-1.6 A. > The 2Fo-Fc and BDP maps are calculated using the same phases. > The metal ion is water hydrated and all the details are crystal clear in > both 2Fo-Fc maps. > The crystals are grown in the presence of Sr and the data sets are > collected at the Sr K-edge. > There are many other Sr sites and all strong peaks in the BDF map overlap > with 2Fo-Fc map peaks perfectly. The Sr site in question is not the > strongest, but it is well above the noise level of the BDF map. > > *Additional information*: > The weird site is actually fully buried inside an internal cavity (it is > surrounded by protein atoms from all sides), but a Sr atom is able to > diffuse into this cavity somehow. All other Sr sites are on the surface of > the protein. > > Any thoughts about why a non-noise BDF map peak would not overlap with a > 2Fo-Fc map peak are welcome! > > Thank you very much, > > Petr > > ------------------ > Petr Leiman > EPFL > BSP 415 > CH-1015 Lausanne > Switzerland > Office: +41 21 69 30 441 > Mobile: +41 79 538 7647 > Fax: +41 21 69 30 422 >
