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CCP4BB  May 2012

CCP4BB May 2012

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Subject:

Re: saxs on xtals

From:

Colin Nave <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Tue, 8 May 2012 17:53:39 +0000

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Jacob, Anna
There are 5 magnetite examples in http://rruff.info/magnetite/ with different elemental compositions.
All similar cells but the data for some is very noisy. R061111 is the least noisy - contains nickel.

Isn't iron stored as ferrihydrite in normal ferritin? Would be interesting to see whether this gives any similar diffuse rings in ferritin single crystal diffraction patterns. People must have checked after all these years. There is even the powder diffraction pattern in Wikipedia (http://en.wikipedia.org/wiki/Ferrihydrite)

The bright spots you refer might be the ones I was fretting about. All diffraction features (rings or spots) should be indexed otherwise the job is incomplete!

Colin



From: Jacob Keller [mailto:[log in to unmask]]
Sent: 08 May 2012 18:29
To: Nave, Colin (DLSLtd,RAL,DIA)
Cc: ccp4bb
Subject: Re: [ccp4bb] saxs on xtals

Dear Colin,
the table you gave seems to have been from  Fe2+Fe3+2O4  or from Fe3-xTixO4. I am curious what the nature of the Fe inside the ferritin is (I don't think it has Ti in it, though...). Is it elemental iron?

Also, to Anna: can you send a picture of that diffraction pattern with spot predictions superimposed? There seem to be some really bright spots which are outliers, and maybe multiple lattices.

JPK
On Tue, May 8, 2012 at 12:21 PM, Colin Nave <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Anna
Yes, you have understood the suggestion.
Could be the 220 and 311 reflections. See for example
http://rruff.info/magnetite/R080025
and
http://rruff.info/repository/sample_child_record_powder/by_minerals/Magnetite__R080025-1__Powder__DIF_File__9448.txt

Trying to index powder patterns from 2 rings is risky and the intensities don't seem to agree.  I guess you don't have higher angle data.

Should be able to evaluate a particle size from the breadth of the rings though. For example a 57A crystal examined with 1A radiation would give broadening of about a degree.

There do seem to be other spots - I guess these are ice rings but you should check. Also be nice to know if apoferritin crystallised under the same conditions (if it can be) shows these rings

Regards
Colin

From: CCP4 bulletin board [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of anna anna
Sent: 08 May 2012 16:55
To: ccp4bb
Subject: Re: [ccp4bb] saxs on xtals
Dear all,
first of all I want to thank you for your attention and all your brilliant suggestions that really cleared my head!!!
Thanks to you (or because of you!!) now I have many ideas and very much to do.

Colin,
 I was just re-considering my diffraction images. Who knows if they are single xtals indeed!
Let's see if I understood your point. Assuming that they are single xtals, if they are located at independent positions in the protein-cage it would be like powder diffraction, with rings at diffraction angles corresponding to magnetite lattice. If they are ordered they should give a diffraction pattern. The corresponding lattice can differ from the protein lattice, do you agree? If this is true, what would I see? Two superimposed diffraction patterns?
Actually, I am not able to evaluate it... I attached one of the diffraction images. It seems to me that there are two diffused rings at about 2.5 and 2.9 A.

Michael, I just read your reply. I think that the eventual periodicity of the partcles can't be completely independent of the protein periodicity (I attached a hypotethical scheme), as you suggest I will try P1.
Once I tryed a naive version of what you suggest: I put a magnet over the xtallization plate. All my collegues made fun of me... :) !!

I will check the literature that you all quoted (hard work!)

Thank you again, new suggestions will be really appreciated.

Cheers,
anna
2012/5/8 R. M. Garavito <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]<mailto:[log in to unmask]>>>
Dear Anna,

I know that you already have gotten replies from some top experts, but your intriguing problem brought up some issues I have run across in the past.

First, from you experience with single crystal diffraction, your results are not that much different from those seen in virus structures where the nucleic acid structure is averaged out.  As the nucleic acid doesn't (and mostly can't) adopt the symmetry of the protein shell, the crystallization process alone does the "averaging."   Just because that ferritin and magnetite have cubic symmetry elements, if they don't line up, the magnetite structure can be "averaged out" upon crystallization.  So, working at lower symmetry may not help, unless there is some directional correlation of the magnetite symmetry and position with the crystal axes.  But try P1 and see what happens.

A second comment is why not try neutron scattering (SANS or single crystal neutron diffraction), particularly as you can match out the protein with D2O and see just the magnetite.  While the same concerns apply for single crystal neutron diffraction, you see more clearly regions of higher average density inside the protein shell.

And lastly, have you tried crystallizing your ferritin/nanoparticle complexes in the presence of a magnetic field?  It would be a neat trick, and people have tried such things in the past, such as for orienting biomolecules.  Some even used old NMR magnets.  Would be wild, if it worked.

Good luck,

Michael

****************************************************************
R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office:  (517) 355-9724<tel:%28517%29%20355-9724><tel:%28517%29%20355-9724>     Lab:  (517) 353-9125<tel:%28517%29%20353-9125><tel:%28517%29%20353-9125>
FAX:  (517) 353-9334<tel:%28517%29%20353-9334><tel:%28517%29%20353-9334>        Email:  [log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]<mailto:[log in to unmask]>>
****************************************************************



On May 7, 2012, at 12:30 PM, anna anna 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 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



--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]<mailto:[log in to unmask]>
*******************************************

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