Thank you all for your suggestions. Finally, I went with pentaethylene glycol (PDB ID: 1PE) and the density looks pretty decent after a couple rounds of refinement (the density "narrows down" and fits the PEG molecule almost perfectly). Regarding the suggestions/assumptions that the density comes from some peptide fragments, I doubt it because (1) my protein is pretty much complete (despite 3-4 AAs at the termini) and (2) modelling a poly-Ala into the density resulted in very poor geometry (and the peptide didn't fit the density).
Thanks again! Cheers Aleks ________________________________ Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> im Auftrag von Martin Noble <martin.no...@newcastle.ac.uk> Gesendet: Donnerstag, 31. August 2023 13:16:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] New density quiz You sure that’s not a stray bit of polypeptide ? On 31 Aug 2023, at 11:54, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. I dont know what it is - but thats a beautiful map! What was in the crystallisation pot, do you know? Eleanor On Tue, 29 Aug 2023 at 18:22, Bijelic, Aleksandar <0000abae22057430-dmarc-requ...@jiscmail.ac.uk<mailto:0000abae22057430-dmarc-requ...@jiscmail.ac.uk>> wrote: Dear CCP4 members, I found the attached density in some of my structures and would highly appreciate suggestions what molecule this could be. The density is always located above an aromatic amino acid and close to the adjacent ASU (like in the attached picture). The mother liquid included MES/Tris as buffer, PEG8000 as precipitant, and ammonium sulfate as additive. Some tartrate "impurity" could also be included. My best guess currently is PEG. Looking forward to your suggestions. Cheers Aleks Von meinem/meiner Galaxy gesendet ________________________________ 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 ________________________________ 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/
