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).
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
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Subject: [ccp4bb] saxs on xtals
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!!