How to interpret P(r) curves

Interactive and automated data processing tools (PRIMUS, GNOM, AUTORG).
Scattering from simple bodies (BODIES), peak analysis (PEAK), data plotting (SASPLOT) etc.
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woodheart
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How to interpret P(r) curves

#1 Post by woodheart » 2016.08.30 17:01

Dear all,

I'm encountering some problems with interpretation of several p(r) curves.

In figure 1, there are three curves representing complexes with three different ATP analogues. How significant is the difference from their p(r) curves?
1.jpg
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Figure 2 shows protein complexes with different RNAs which is expected to be the same. Could the difference between the curves be caused by the improper subtraction? These two experiments were conducted from different trips and there were some changes in the instrument setup. Is there any chance that's the cause of the difference?
2.jpg
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The last figure shows two curves representing protein complexed with two RNAs the only difference between which is one with modification on the other end of protein binding site. That's shouldn't affect the protein-RNA interaction. Curve 1 has a wider peak and bigger Dmax. The protein is big (>100kDa), so it's impossible to be a dimer for curve 1. How should I interpret the curves?
3.jpg
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Thank you very much,
Xiaoming

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AL
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Re: How to interpret P(r) curves

#2 Post by AL » 2016.08.31 13:22

woodheart wrote:In figure 1, there are three curves representing complexes with three different ATP analogues. How significant is the difference from their p(r) curves?
I'd say not significant at all. I'd compare the original SAXS data and not the p(r).
woodheart wrote:Figure 2 shows protein complexes with different RNAs which is expected to be the same. Could the difference between the curves be caused by the improper subtraction?
Yes, this is quite likely. Again, I'd compare the SAXS data. You may scale and add a constant to one of the curves to minimize possible background subtraction effects (using DATADJUST or the Adjust button in PRIMUS).
woodheart wrote:The last figure shows two curves representing protein complexed with two RNAs the only difference between which is one with modification on the other end of protein binding site. That's shouldn't affect the protein-RNA interaction. Curve 1 has a wider peak and bigger Dmax. The protein is big (>100kDa), so it's impossible to be a dimer for curve 1. How should I interpret the curves?
You should come up with models which would fit both SAXS data sets.

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