Small Angle X-ray (SAXS) Scatting Data Processing
Below is an overview of the programs that we used during Small Angle X-ray Scattering (SAXS) data processing. This should help clear up how a number of SAXS programs relate to each other (this is not all inclusive).
Overall, I feel like there is some hand waiving in regards to the consistency of the results from the SAXS data processing programs. However, if you cannot attain a crystal of your macromolecule then this biophysical method is probably worth trying.
A quick introduction into what is needed for a SAXS experiment? In addition, you should contact your respective beam line scientist.
The following links are for more detailed information about the programs mentioned above:
Crysol – generates scattering curves from crystal structures
SASREF – rigid body modeling from crysol (see above)
Primus – low resolution data, Guinier plot
IGOR – low resolution data, Guinier plot
GNOM – uses all scattering data as a distrubtion function to determine the shape of the protein
Gasbor – all Q, chain dummy atoms
Dammin – low Q, using dummy atoms
Supcomb – aligns mutiple models to find the most probable
Damaver – aligns mutiple models to find the most probable
Credo/Chadd/Gloopy – model in missing domains
If you end up getting really stuck there is a forum that maybe able to help. Finally, I would like to thank, Jen, for working through these programs.
What_Saxs?
May 17th, 2009 at 3:11 PM #
Why would I want to use SAXS? How detailed biological question am I answering? For kinetics, at what time resolution can I use SAXS?
Could you give examples where SAXS has been more informative than EM, ultracentrifugation etc? If possible cite some papers that would give us an idea of what can be done. Never used it, but seen a few talks where I wondered why they are doing it (”arbitrary” fit of model to data).
Sean
May 17th, 2009 at 4:30 PM #
You may want to use SAXS if you want to know how two proteins interact.
SAXS yields a molecular envelope so not quite as detailed as crystallography.
This is an example of a molecular envelope that was used to study a protein complex.
We did not look into kinetics, but from the papers that I have looked at it is in the minutes timescale (phenomenon like protein complexation and aggregation).
SAXS is done in solution unlike EM (we have not done EM so take this with a grain of salt)
SAXS can tell you points of interaction unlike in UC.
The talks that I have seen are the same and think the ‘arbitrary’ fitting is partly due to the consistency of the data processing. The resolution yields a molecular envelope which can allow for quite a bit of play in the orientation of a particle protein.
Sean
July 22nd, 2009 at 11:18 PM #
SAXS to put an end to crystallography?
http://www.azonano.com/news.asp?newsID=12674