Hi Sayan Looks interesting. My first thought was a metal ion with attendant waters, but it doesn't look quite right for Trigonal co-ordination - maybe trigonal bi-pryamidal with a missing/poorly defined ligand above the plane in image 1?
A couple of questions to help refine the search: 1. What is the distance from the centre of the nearest positive density blob to an Oxygen in the Asp sidechain? 2. What are the distances from the middle of the central blob to the centres of the surrounding blobs? 3. do you have enough data to make an anomalous difference map? 4. What was in the crystallisation conditions (thinking specifically about cations - any Mg2+, Ca2+?) Good luck! Dave -- Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Sayan Saha <ssaha43...@gmail.com> Sent: 30 June 2022 08:03 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Unidentified electron density External Sender: Use caution. Dear All, I am trying to refine a protein structure. I observed an additional electron density (Figures attached) connected to the aspartate residue. Any suggestion in this regard would be appreciated. With best regards, Sayan Saha. ________________________________ 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=05%7C01%7C%7C042cfd1dea0d4f67b85508da5a680c1e%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637921700191446497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7C&sdata=pa9PZ8XiC6OSMwweMqwJCLxoSM2AgQExz1EPlBKfEnM%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/
