Hi, 1) maybe work on refining the protein structure first, so that your residual maps improve in quality. 2) Maybe only part of the peptide is ordered? Can you assign part of the sequence? Starting a bulky aromatic (e.g. W/Trip)? 3) do you have a way to QC your peptide? Is it still 11 residues in your crystallisation solution?
Cheers Greg On Thu, 27 Feb 2025, 21:10 Manjula Ramu, <manjula....@gmail.com> wrote: > Dear all, > > I recently solved a complex structure of a protein with an 11-amino-acid > phosphopeptide at 2.58 Å resolution. The asymmetric unit contains two > protein chains, and the difference map shows positive green density (Fo-Fc > positive difference density) for the peptide. However, the density is not > well-defined, making manual fitting of the peptide challenging. > > I have two key questions: > > 1. *How can I generate a 3D model of the 11-residue phosphopeptide?* > 2. *What options are available for fitting the peptide into the > electron density?* > > I would greatly appreciate any guidance or suggestions to help complete my > structure. I have attached the png file from the coot. > > ---------------------------------------------------- > > Thanks and Regards, > > *Manjula * > > > > > > <https://www.nimhans.kar.nic.in/> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
