Molecular Weight estimation using Shape&Size method

[Isabel Elliott]

Hi Jesse,

I have a number of proteins that I have collected SAXS data for, and have been using the Molecular Weight tab to estimate the MW. For the Shape&Size method, I have mostly been getting reasonable results however for one of my proteins, I consistently get an MW from the Shape&Size method of -1.00E+00 kDa and I am expecting an MW of approx 90-100 kDa. For my other proteins, where Shape&Size works well, the DATCLASS shape classification is 'flat' whereas for this one which doesn't work it is 'random-chain'. The DATCLASS Dmax comes out as -1, whereas I am expecting a value of 140-160. I know that this protein is more flexible than the others I have measured - would this be causing the unusual results? Or is there likely something else going wrong with the algorithm?

Thanks,

Isabel Elliott

[Jesse Hopkins]

Hi Isabel,

The Shape&Size/DATCLASS method only works for rigid systems. It's based on a ML method that used the protein structures in the PDB, assuming rigid shapes, so if the classification determines that the system is flexible (e.g. random chain classification) it doesn't return a result. It's also less reliable for flexible proteins in general, even if it does return a result, for flexible systems I'd recommend looking more to the Vc method.

You can find more information on the different MW methods (including links to the original papers) here:

https://bioxtas-raw.readthedocs.io/en/latest/saxs/saxs_mw.html

Hope that helps.

All the best.

- Jesse

----

Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

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[Isabel Elliott]

Hi Jesse,

That makes sense - thank you very much for the explanation.

Best wishes,

Isabel