sharp minimum in calculated curve

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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cmetrick
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sharp minimum in calculated curve

#1 Post by cmetrick » 2017.07.18 22:41

Hi all,

My labmates and I have been seeing a strange characteristic in post processing experiments for unrelated proteins and haven't worked out the pattern yet. We see a sharp dip in the calculated SAXS curve not evident in experimental data. In my case, I study a protein made of two globular domains (with crystal structures) separated by an 80aa linker with unknown structure and binding characteristics. Below I have two fits from EOM for one data set processed with or without an input PDB file. The data is from the NTD+linker construct so the PDB is for the NTD.

No PDB
Image

With PDB
Image

I've see this in CORAL as well. Clearly it has to do with the inclusion of a PDB file, but I've used the same file with data for full length constructs and only seen "the dip" occasionally. Like I said, my lab mates have seen it in their data for very different proteins as well.

Has anyone see and/or sorted this before?

Thanks!

cmetrick
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Re: sharp minimum in calculated curve

#2 Post by cmetrick » 2017.07.19 17:54

Update: My labmate has also seen this without putting in a crystal structure. Any hints?

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AL
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Re: sharp minimum in calculated curve

#3 Post by AL » 2017.07.20 14:07

cmetrick wrote:We see a sharp dip in the calculated SAXS curve not evident in experimental data.
Probably the fit contains a negative point. This happens in some programs when it is not possible to obtain a decent fit.

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