Thanks to all who replied to my message. The most logical explanation to the observed phenomenon is likely the following. During crystallization, Sr ions from the crystallization solution kick out a fraction of the Mg(OH)6 ions from the binding site in question. The cavity of the binding site is big and the Sr ion binds at a slightly different position compared to the Mg(OH)6 ion. The BDF map shows the shifted position of the Sr ion, whereas the 2Fo-Fc map shows the position of the Mg(OH)6 ion. This is possible because the occupancy of the Sr ion at that site is low - the height of the Sr peak in the BDF map is less than 15% of the maximal peak height - and the contribution of the Sr ion to the 2Fo-Fc map is negligibly small. The “normal” (2Fo-Fc) scattering of the Sr ion is essentially completely masked by the Mg(OH)6 ion scattering because the two overlap (they are 0.47 A apart) and the latter has a 5-6 times higher occupancy.
Eleanor’s and Phoebe Rice’s comments were extremely useful in solving this puzzle (at least for me - we will see if the referees agree that this is a solution). This particular comment by Phoebe was really insightful considering she did not see the actual data but only read my somewhat incomplete description: “Could it be a mix of species - partly Sr and partly some non-anomalous-scattering entity that sits in a slightly shifted position?” CCP4BB is an incredible resource full of really clever people! Thanks to all again! Petr On Apr 24, 2014, at 11:39, Petr Leiman <petr.lei...@epfl.ch<mailto: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
