In theory, there should be a simple way to calculate P(r) directly from the 
crystal structure rather than indirectly from the expected scattering curve. 
Distribution of pair distances, r^2 weighted. This would remove any ambiguity 
about choice of Dmax.  ... but I can't think of any of the common SAXS programs 
that do it that way. Clearly, since you have the crystal structure, you know 
the exact Dmax (the maximum diameter of the object). I would use the maximum 
atom pair distance from the crystal structure, then add a little bit to account 
for the width of the atoms and solvation layer.  Do this only for the 
theoretical curve. The Dmax for the solution structure may be different due to 
conformational fluctuations. Dmax is not a well-defined quantity in reality and 
has a large error range.

I would describe the feature you see in the theoretical P(r) at 70A as a 
"shoulder." Such a feature in a dimer is not surprising because you have two 
large domains separated by a distance. Do you see it in the monomer P(r)?  The 
fact that it is smoother in the solution data is also not surprising, since you 
can expect domains to move around on average. Some programs actually attempt to 
model this kind of disorder by sampling conformation space to see which various 
conformations best fit the curve. Probably that's more analysis than would be 
useful to you.

Richard

> On Jun 17, 2012, at 1:11 AM, Xun Lu wrote:
> 
>> Drs.Caldwell, Briggs, and Gupta,
>> 
>>   Thank you very much for the advices.   I regret that I didn't show any 
>> figure in the earlier post.  Here I've attached a figure showing the data 
>> quality and some fittings.  
>>   Data look OK, right? This question may sound silly, but I just want to 
>> make sure.  
>>   As I said in the earlier post, I tried Crysol.  I used the crystal 
>> structure (dimer+DNA) as the model, and the fitting was OK, right?  In fact, 
>> I also tried monomer+DNA as the model (I simply deleted one monomer from the 
>> PDB file).  This kind of comparison may be meaningless, but I was just 
>> curious.  I am wondering how people judge whether the fit is good or not.    
>> 
>>    Another question, I tried to generate an envelope from SAXS data using 
>> Gasbor and Dammin (people say Dammin is better at protein-DNA complex, 
>> although it still uses the same bead for both DNA and protein?).  The 
>> generated envelope was nothing like my crystal structure.  As people have 
>> pointed out, protein and DNA scatter differently.  SANS is the way to go.  
>> So I should give up on modeling SAXS data?  I've almost given up, because 
>> anyways I have the crystal structure, and SAXS is only a small part of this 
>> paper.  
>> 
>> 
>> 
>> Thanks,
>> 
>> Xun
>> 
>> 
> 

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