Re: [ccp4bb] saxs on xtals

[anna anna]

Thanks to all again! Find below my answers/comments to all your replies.

Colin Nave,
I'll certainly collect higher resolution dataset to look for more
diagnostic rings.
Apo-ferritin xtallizes in the same conditions with the same cell (I know it
from literature), I'll measure it too, to look for differences.

Jacob Keller,
we loaded ferritin with Fe and Co and oxidized them obtaining
CoxFe(3-x)O4/Fe2O3.
About the brillant spots, by eye  I attributed them to eventual ammonium
sulfate xtals (2M in xtallization conditions) but it could be something
else, compare to apo-ferritin will help.

James Holton,
I didn't think about it! Actually it's the same as nuclear spin in NMR: the
orientation is random until an external magnetic field is applied. It would
be very very interesting to collect diffraction under this condition, do
you know an equipped beamline?

Allister Crow,
thanks for encouragement! I knew that someone had already studied it...
your paper is very usefull. Myabe my case is different because I have Fe3O4
and an external magnetic field could induce order, I hope I can do this
kind of experiment.

John Hellywell,
I'll certainly measure at higer resolution.
Ferritin should be fully loaded since there are about 3500 metal atoms per
protein shell.

I'll keep you updated on my future results!

Re: [ccp4bb] saxs on xtals

[Jrh]

Dear Anna,
Very interesting diffraction pattern.
Any chance of measuring to higher resolution?
Ie to try and capture the higher order rings, which presumably are there.
Also interesting that these rings seem quite weak ie the ferritin perhaps not 
fully loaded?
Best wishes,
John


Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 8 May 2012, at 16:54, anna anna  wrote:

> 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 
> 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 Lab:  (517) 353-9125
> FAX:  (517) 353-9334Email:  rmgarav...@gmail.com
> 
> 
> 
> 
> 
> 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 

Re: [ccp4bb] saxs on xtals

[Colin Nave]

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. R06 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:j-kell...@fsm.northwestern.edu]
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 
mailto:colin.n...@diamond.ac.uk>> 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:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] 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 
mailto:rmgarav...@gmail.com><mailto:rmgarav...@gmail.com<mailto:rmgarav...@gmail.com>>>
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

Re: [ccp4bb] saxs on xtals

[James Holton]

Seems to me that if you really do have a little magnet inside your 
ferritin you would expect the protein crystal to behave like a "spin 
glass".  Spin glasses are a classic homework problem in statistical 
thermodynamics that makes most students question their choice of major.
However, invoking them is also a good way to impress physicists and get 
you beam time.  The most bizzare thing about spin glasses is that they 
can actually have negative temperatures, but I digress.


In a nutshell:  Any "ordering up" of the little magnetite nanocrystal 
orientations must not just work against "entropy", but also against the 
magnetic fields of all its neighbors.  If they were all aligned 
(ordered) then each magnet is oriented the "wrong way" in a massive 
field generated by all the other magnets, so there is a very strong 
incentive for each of them to turn over.  But then once a lot of them 
have randomly turned over the situation gets a lot more complicated.  
Ideally, the lowest-energy state is where the magnets exactly alternate: 
up, down, up, down, up, down all the way through the crystal.  However, 
in reality there is essentially no pathway for the magnets to "find" 
this orientation, so they never do.  The system is "frustrated" (and 
yes, that is the official term).


So, in a way, you have a lot of reasons to expect that the iron core of 
the ferritin will be "disordered", but you should be able to perturb 
this "disorder" with a strong enough magnetic field.  Not sure how 
strong you need, but there will also be a temperature where the magnets 
cannot rotate anymore, so perhaps plunge-cooling into the liquid helium 
inside a superconducting magnet is what you want to "shoot for".  But, 
then again, it could be as simple as exposing a crystal to a relatively 
"weak" magnetic field at a temperature just above the glass transition 
of whatever shares the lumen of the ferritin sphere with the 
nanocrystal.  Probably somewhere around 130 to 160 K.  Warkentin & 
Thorne (2009) presented a potentially general way of holding a protein 
crystal at any temperature you want between 100 and 300K: 
http://dx.doi.org/10.1107/S0021889809023553


-James Holton
MAD Scientist

On 5/8/2012 7:16 AM, R. M. Garavito wrote:

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) 355-9724Lab:(517) 353-9125/
/FAX:(517) 353-9334Email:  rmgarav...@gmail.com 
/

//




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 /s/axs th

Re: [ccp4bb] saxs on xtals

[Jacob Keller]

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 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:CCP4BB@JISCMAIL.AC.UK] 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 mailto:rmgarav...@gmail.com
> >>
> 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 

Re: [ccp4bb] saxs on xtals

[Colin Nave]

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:CCP4BB@JISCMAIL.AC.UK] 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 mailto:rmgarav...@gmail.com>>
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 Lab:  (517) 
353-9125
FAX:  (517) 353-9334Email:  
rmgarav...@gmail.com<mailto:garav...@gmail.com>




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 XR

Re: [ccp4bb] saxs on xtals

[R. M. Garavito]

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 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





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
> 
> 
> 
> 
> 

Re: [ccp4bb] saxs on xtals

[Colin Nave]

Anna
Are the nanoparticles expected to be single crystals? Magnetite has Fd3m space 
group with a 8.4A lattice (just looked it up). This should give some 
diffraction features such as broad spots (broadened because of the small 
particle size) or rings (if there is no alignment between the nanoparticles). 
Have you looked for such effects in the diffraction patterns which you already 
have from the single crystals?

Colin

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of anna anna
Sent: 07 May 2012 17:30
To: ccp4bb
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

Re: [ccp4bb] saxs on xtals

[Jrh]

Dear Anna,
The reprint:-
http://www.sciencedirect.com/science/article/pii/S0020169300822689
has some bearing on your query.
Best wishes,
John
Prof John R Helliwell DSc 
 
 

On 7 May 2012, at 17:30, 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
> 
> 
> 
> 
> 

Re: [ccp4bb] saxs on xtals

[Colin Nave]

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:CCP4BB@JISCMAIL.AC.UK] 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of anna anna 
[marmottalb...@gmail.com]
Sent: Monday, May 07, 2012 5:30 PM
To: CCP4BB@JISCMAIL.AC.UK
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 m

Re: [ccp4bb] saxs on xtals

[Edward Snell]

Hi Anna,

There has been some nice single crystal SAXS work done, check out J. Mol. Biol 
(1998) 284, 1439-1452 "Imaging RNA and Dynamic Protein Segments with 
Low-resolution Virus Crystallography: Experimental Design, Data Processing and 
Implications of Electron Density Maps" by Tsuruta et al. There is the 
capability to study single crystals on SAXS lines - in this case 4-2 at SSRL.  
However if you desperately need to use crystals, you may be better served with 
a single one by moving the beamstop back, choosing a lower energy and trying to 
collect all the low resolution diffraction information from a single crystal. 
You can truncate the high resolution data and see if you start to see 
information from the  particles if there is some ordering. Even better if you 
can compare it from a crystal without them if it's in the same space group.

Have you thought about the possibility of anomalous SAXS with and without doped 
ferritin?

Note that you may be inducing interparticle effects which will complicate the 
interpretation of any SAXS data, solution or suspended crystals.

Cheers,,

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Senior Scientist, Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of anna anna
Sent: Monday, May 07, 2012 12:30 PM
To: CCP4BB@JISCMAIL.AC.UK
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

Re: [ccp4bb] saxs on xtals

[Murray, James W]

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 [CCP4BB@JISCMAIL.AC.UK] on behalf of anna anna 
[marmottalb...@gmail.com]
Sent: Monday, May 07, 2012 5:30 PM
To: CCP4BB@JISCMAIL.AC.UK
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

Re: [ccp4bb] saxs on xtals

[Jacob Keller]

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  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
***

Re: [ccp4bb] saxs on xtals

[Lucas]

2012/5/7 David Schuller :
> That sounds like powder diffraction.

That was also my impression. There are at least two groups doing
interesting things on this subject - Andy Fitch/Irene Margiolaki at
ESRF and Robert von Dreele at APS. I've contacted the first group
after meeting Andy Fitch in a XRD symposium some years ago (2005, I
think) and they were very kind to provide many hints on sample
preparation, which seems to be the hardest thing to do in those cases.
We are tempted to think "oh, so do I simply need to harvest a whole
lot of small crystals in a loop and everything will be fine?", but it
is a bit trickier than that. I am pretty sure they will be able to
provide some hints to Anna's case, which seems very similar to a
powder diffraction experiment.

Lucas Bleicher

Re: [ccp4bb] saxs on xtals

[David Schuller]

That sounds like powder diffraction.

On 05/07/12 12:30, 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 /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








--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] saxs on xtals

[anna anna]

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