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Anna Interesting. Yes, the cryo-em might be the way to go to see if some structures (i.e. not just spheres) within the protein shell are aligned. The SAXS study does make some sense. If the magnetic particles have some alignment this should manifest itself in the SAXS pattern, with the precise effects depending on the correlation length (how far the alignment extends). This really requires SAXS, not WAXS which would not be sensitive to the long range effects you wish to see. As you suggest, it would also be good fun (and perhaps even informative) to do this on single crystals. A coherent x-ray beam, using CDI or ptychography (search for these terms or contact me if you want some details) could be employed if you restrict yourself to crystals of a few microns in size. One can even play around with absorption edges/anomalous dispersion/magnetic resonance (for single crystals or powders) as I understand the interest is in magnetic phenomena. Making resonant soft x-ray scattering measurements at the oxygen K edge have been used for studying magnetite. The polarisation of the x-rays could be exploited. Our neutron friends can also study magnetic effects but I don't know about sample size requirements. Doing the measurements in a strong magnetic field might be interesting. If the samples are easy to prepare, I would start from collecting the lowest hkl reflections from single crystals to check you are not missing anything. Then a low angle SAXS pattern as suggested by your collaborators. After this consider the other suggestions which are rather speculative and not really routine. Good luck Colin -----Original Message----- From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Murray, James W Sent: 07 May 2012 19:25 To: ccp4bb Subject: Re: [ccp4bb] saxs on xtals Dear Anna, I once modified CNS to refine two solvent regions of ferritin, one inside and one outside the shell. Perhaps this can be done in Phenix now. If you want to locate magnetite particles in this way, you should collect data to as low a resolution as you can (may need to move backstop), as this is where the solvent has most effect. I would also collect control data with apo and holo ferritin to compare. However a much easier way may be to directly visualise the particles in cryoEM. I have seen very nice micrographs of particles inside ferritin (can't remember ref now). best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 ________________________________________ From: CCP4 bulletin board [[log in to unmask]] on behalf of anna anna [[log in to unmask]] Sent: Monday, May 07, 2012 5:30 PM To: [log in to unmask] Subject: [ccp4bb] saxs on xtals 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 saxs that I can't see by waxs?? 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