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
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