SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry

Small angle scattering software (except ATSAS)
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cjuark
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SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry

#1 Post by cjuark » 2020.04.22 17:44

To the SAXS community,

This question involves the Guinier approximation of Rg in a protein, with the help of SCATTER IV. I am currently trying to assess changes in the dynamic flexibility in a sequentially bound three domain protein held by flexible linkers, as a function of calcium concentration. The overall protein may be assumed to be rod like.

After assessing the Rg of 5 different samples, differing in calcium concentration signified as pCa, I had SCATTER IV produce a normalized kratky. All is well in the normalized kratky aside from my sample "7" where it exhibits a peak at an X value of 3.5. On the other hand, my other four samples each peak at around an X value of 4.5. After several rounds of refining and re-calculations, I continue to get the same results. It is my understanding that each sample should peak similarly in a normalized kratky.

What does this difference in peaks represent for my "7" sample (black), and does it have to do with variation in I(o) and/or Rg? Is SCATTER IV optimized for more globular proteins, or is it sufficient for rod like proteins? I have attached a picture of my normalized kratky in addition to the color key of my samples.

In addition, I am also looking for tips in manually calculating the Rg of samples, in excel, from raw .dat files. Any tips or best practices for this are appreciated, but not necessary. Thank you all!
Attachments
Screen Shot 2020-04-22 at 9.54.03 AM.png
color key for norm kratky.
Screen Shot 2020-04-22 at 9.54.03 AM.png (20.82 KiB) Viewed 142 times
pca series norm kratky.png
norm kratky for pca series 3 through 7
pca series norm kratky.png (171.51 KiB) Viewed 142 times

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AL
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AUTORG

#2 Post by AL » 2020.05.11 11:08

cjuark wrote:
2020.04.22 17:44
In addition, I am also looking for tips in manually calculating the Rg of samples, in excel, from raw .dat files. Any tips or best practices for this are appreciated, but not necessary.
Excel might be a bit challenging.
Try ATSAS AUTORG for an automatic Guinier approximation or DATRG for calculating the Guinier Rg from a given interval. You may consider using the Rg computed from the pair distance distribution function p(r) (provided its Fourier transform fits the experimental data).

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