A technecality - the Dano only contains information about anomalous scatterers and should therefore show these more precisely.
The 2Fo-Fc map will tend to show anything which is included in the phasing at the position given. For safety you can set all the atom occupancies in the vicinity of the site to 0.00 and then use phases calculated from the edited structure to check again. ... This sort of thing sometimes happens with the Se of MSE, and the explanation there is that the MSE is in more than one conformation.. Eleanor On 24 April 2014 10:39, 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 > >
