It might be that the "bulk solvent correction" is nullifying the interior of the ferritin structure, and there should be a way to tell the refinement software not to treat the interior as solvent. Perhaps then you might find your Fe? Also, I would think there should be some powder-like diffraction rings in the background of the ferritin crystal diffraction corresponding to the scattering from the jumbled but crystalline Fe in the inside--did you see any extra rings in the background of your original diffraction data? Not sure what the Fe-Fe distance is in this case in particular, but there should be a ring (or rings) corresponding to that (those) distance(s)....
JPK On Mon, May 7, 2012 at 11:30 AM, anna anna <marmottalb...@gmail.com> wrote: > Dear all, > I'd like some suggestions/opinions about the sense of an experiment > proposed by a collaborator expert in saxs. > In few words, he wants to collect SAXS data on a suspension of protein > xtals to investigate "low resolution periodicity" of the xtal (more details > below). > The experiment requires a very huge number of xtals to obtain the circles > typical of saxs and it is very time-consuming to me (I know nothing about > saxs, I have only to prepare the sample). I proposed to measure a single > rotating xtal (like in XRD) but he told they don't have a goniometer on > saxs beamline. > Here is my concern: does it make sense to measure many xtals together? > Don't we lose information with respect to single xtal? And, most of all, > what can I see by *s*axs that I can't see by* w*axs?? > Sorry for the almost off-topic question but I think that only someone who > knows both the techniques can help me!! > > > Some detail for who is intrigued by my story: > we prepared doped magnetite nanoparticles using ferritin as bioreactor. I > crystallized this spheres filled with metal and solved the structure at > 3.7A but I can see only the protein shell while there is no density inside, > even if I know that the nanoparticles are there. A simple explanation is > that the particles are free to move in the cavity(note that the diameter of > the nanoparticle is shorter then the inner diameter of the protein shell), > ie are disordered, and do not contribute to diffraction, in fact, to my > knowledge, nobody have ever seen the metal core inside ferritin or dps > proteins. However, since they are magnetic particles they must "see" each > other through the protein wall, ie they can't be completely free to move in > the cavity. Maybe, but this is just my opinion, I don't see the particle > because the "period of the particle" in the xtal is different/longer than > the period of the protein shell. > Anyway, we are interested in the relative distance between the magnetic > particles in the xtal to study the effects of magnetostatic interactions in > nanoparticles 3D arrays. We are going to do this by saxs since, they told > me, lower resolution is useful in studying this long range periodicity (the > diameter of ferritin is about 120A) but it seems fool to me using a > suspension of so many xtals to obtain a scattering curve while I could > collect diffraction images from a single xtal!!! I know that saxs is used > when you don't have xtals but if you have xtals, ie your system is ordered, > xtallography is much more powerful!! > > Another question: how can I handle my diffraction data at 3.7A resolution > to "look for" nanoparticles? Should I try a lower symmetry? Maybe the > anomalous signal? Have you any reference for a similar case? > > Thank you very much!! > > anna > > > > > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
