Dear Nick, I would contact some MassSpec people and ask if they could find out the mass of your mystery ligand. I would also carefully look at the neighboring protein. It might be an alternate conformation of a partially disordered loop. Finally, I would check literature to see if a natural ligand/cofactor of your protein would fit. However, your ligand seems to be bound in a crystal contact so it may be an artifact.
Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Nick Thomas Gesendet: Mittwoch, 14. Juni 2017 18:40 An: [email protected] Betreff: [ccp4bb] Unknown Ligand Density Dear CCP4bb, I am refining a structure and have come across strong electron density for an unknown ligand (image attached). Would someone be able to identify this unknown ligand that somehow was co-purified with the protein. The electron density shape does not match anything included in the crystallization conditions. The crystallization condition is 0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate
