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That is correct. We saw this in every selenomethionyl protein structure that was determined at CESG. There are two reasons for the negative density defects at Se atoms. As you note, the default scattering factors for Se are incorrect for these experiments, as f' is large in Se SAD experiments. Additionally, the fractional incorporation of Se is often less than 100%. For our autoinduction media, it was fairly consistently around 90 mole percent Se. Your mileage will vary on the last effect. In addition to these two effects, which are particular to SeMet around the Se K edge, both regular methionine and selenomethionine have somewhat disordered sidechain conformations more often than you might guess (without anomalous diffraction data poking you in the eye and showing definitively that the Se is in more than one place.) On Oct 31, 2011, at 10:57 AM, Ivan Shabalin wrote: > I noticed that if I refine a structure containing SeMet, then Se atoms usually have big negative (red) peeks of difference map and high B-factors. As I understand from the diffraction theory and from some discussions at CCP4bb, that may result because in REFMAC the atomic scattering factors are internally coded for copper radiation (CuKa).