Update: I tried more anomalous maps, this time with the originally-deposited data at 1.8 Ang (mine were similar, substrate-soaked crystals) and phases from the refined model, and the Se sites are now ~40-50 sigma, and there is still totally nothing at the Cl and S sites, even though in 2Fo-Fc the Cl is ~9 sigma, and the S is 8 sigma (the Se is ~15 sigma). If it has reasonably-high electron density, shouldn't it have at least some anomalous scattering? I am wondering whether somehow the model phases are biasing the map, but I can't really imagine how that would be...
JPK On Thu, Sep 1, 2011 at 3:15 PM, Bosch, Juergen <jubo...@jhsph.edu> wrote: > Where in refinement of your model are you ? > At an early stage I wouldn't be surprised to only see SeMets but once you've > refined your structure and go back to calculate an anomalous map with the > improved phases you might double your signal for SeMet and start seeing > sulfurs. > An alternative explanation, you've blasted your crystals at the synchrotron > and the remaining anomalous signal is too weak to show the sulfurs. > Just two thoughts, > Jürgen > On Sep 1, 2011, at 4:03 PM, Jacob Keller wrote: > > Dear Crystallographers, > > I recently have been working with a 2.5 Ang SeMet peak wavelength > dataset which contains 2 cys's and also a couple of bona fide Cl ions > (reasonable b-factor/site is semi-buried/water does not work). In the > FFT anomalous difference map using PhiC from the refined model and > Dano, I can see the MSE's at ~10 sigma, but no Cl ions, even though Cl > should have f" = ~0.3 versus Se's f" = ~4, and no S's in the cys, > despite f" = 0.23e. There is really no anomalous peak at all--is it > just the smallness of the signal, or are the Se's somehow "swamping > out" the other signal? Perhaps the phases are tainted by the presence > of semet in the model? > > Looking for suggestions, > > Jacob Keller > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > cel: 773.608.9185 > email: j-kell...@northwestern.edu > ******************************************* > > ...................... > Jürgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://web.mac.com/bosch_lab/ > > > > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
