|Topic:||protein peptide complex scattering profile .|
|Details:|| I am dealing with a protein-peptide complex. when i compared my experimental curves with theoretical curve computed by crysol,i was wondering what contrast should i substract, buffer vs buffer with peptide.?
the atoms of the peptide are also included in the pdb file, would the crysol take the contribution of the peptide into
Posted by: ckerr
2017-11-14 21:46:28 MST
| You should aim to subtract what is left in the buffer after [some of] the peptide has bound to the protein. If the concentration ratio is 1:1 then there is no free peptide left after binding, so you should subtract the buffer without peptide. If you have a large excess of peptide then the concentration in the buffer is almost the same as before binding, so you should subtract the buffer with peptide.
CRYSOL will by default use all ATOM and HETATM records in a PDB file which are not waters, explicit hydrogens, or rotamer alternatives of atoms which have already been read. So if the peptide is in the PDB file it will be included in the calculated scattering.
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