Hi Xun, it is difficult to judge without seeing the P(r) plots, but seeing as you have a dimer in your crystal structure and a dimer in your SAXS, AND your Chi2 value seems reasonable for a good match between PX and SAXS, I'd say you've got what you need.
A matching P(r) plot would be nice, but the crysol plot comparing your SAXS scattering curve and the theoretical scattering curve from your crystal structure should be enough for a figure. HTH, Dave ============================ David C. Briggs PhD Father, Structural Biologist and Sceptic ============================ University of Manchester E-mail: [email protected] ============================ Webs : http://flavors.me/xtaldave Twitter: @xtaldave Skype: DocDCB ============================ On 16 June 2012 19:29, Xun Lu <[email protected]> wrote: > Dear all, > > > I have solved a protein-DNA structure, and I also did SAXS to get some > ideas of the solution structure. The SAXS data were good, no aggregation at > all three tested concentrations. I tried to use Crysol to see if my crystal > structure fits the SAXS. The fitting to the scattering profile seems good to > me and the Chi2 is 1~1.4. Then I wanted to see how the P(r) looked like > (wanted to make a figure for my paper:). I calculated the theoretical > scattering profile of the crystal structure from an online server (FOXS). I > then run GNOM to make P(r). To my surprise, this theoretical P(r) looks a > little different from the P(r) of SAXS data. There's a very small bump that > was peaked at 70A (Dmax is 108A, which seems reasonable from the crystal > structure). The major peak was at 25A. As some people said, P(r) is indeed > quite sensitive to subtle differences. > > The protein is a dimer in the crystal, although it can also bind DNA > as a monomer (much more loosely). The estimated MW from SAXS indicates it's > a dimer in solution as well. It seems that I got the information I wanted > from the SAXS experiment, but maybe not. Due to the low resolution of SAXS, > maybe I can only say that the majority is a dimer?? Would it be possible to > see the monomer if there's only 10% of them in the solution? How to > interpret the discrepancy between the P(r) from crystal and the P(r) from > SAXS? > > > Any comments are welcome! > > > > > Xun > > > Sent from my iPad
