Hi Samer, Did you use a His tag/Ni-NTA during purification? Sometimes Ni2+ ions leach off the Ni-NTA - maybe the two "ears" are accompanying waters?
Ni-His co-ordination distance is pretty short (2-2.2Å - table 3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872550/#!po=0.694444) and might account for your bump when you model in a ligand. Good luck! Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Nils Marechal <[email protected]> Sent: Monday, July 20, 2020 5:27:37 PM To: [email protected] <[email protected]> Subject: Re: [ccp4bb] electron density close Histidine side chain Dear Samer, What king of cryo-protectant did you use ? Such a bent density, with that size, looks like an ethylene-diol. Best regards, Nils Marechal De : "samer halabi" <[email protected]> A : [email protected] Envoyé: lundi 20 Juillet 2020 18:17 Objet : [ccp4bb] electron density close Histidine side chain Hello all, I have few blobs in an MHC II structure I am working on, especially opposite to Histidine as in the accompanying screenshot, that I am confused about. In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol. Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which makes me think whether there is a covalent bond forming between Histidine and other molecule. Perhaps by oxidation. I would greatly appreciate if you can advice me about it, whether there is some kind of ligand I can try to fit and if this is something that occurs in some structures. Thank you. Best regards, Samer ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cd74e8619d6764702ee3b08d82ccb746e%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637308599631231459&sdata=sX3KQ8eDIeGJiBFCc%2FwuELQBXUB9A1CL8XXtSaZBiEU%3D&reserved=0> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cd74e8619d6764702ee3b08d82ccb746e%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637308599631231459&sdata=sX3KQ8eDIeGJiBFCc%2FwuELQBXUB9A1CL8XXtSaZBiEU%3D&reserved=0> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## 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/
