Hi Maria, from the picture, it looks like disorder to me. Note that the three non-H atoms at the top of the ring also have significantly less density than the five non-H atoms that are closer to the protein. Perhaps the compounds is just quite wobbly in it's binding site.
Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es/~mjvanraaij Section Editor of Acta Crystallographica F, Structural Biology Communications http://journals.iucr.org/f/ > On 26 Feb 2019, at 13:38, Maria Håkansson <maria.hakans...@saromics.com> > wrote: > > Dear all, > > We have experienced nitril groups not present in the electron density > after data collection on compounds bound to different proteins. > > In one of the projects the compound was tested by MS to check that > the nitril is present in solution before data collection (crystals used to > for MS analysis). > The nitril should be present since the molecular weight of the compound is > the same. > > Also the crystals have been exposed using 10% of the beam (instead of 100%) > to try to make > the effect of radiation damage as small as possible. Still the nitril is not > present. > > In both cases the nitril atoms have been modeled with high temperature > factors but > the electron density is missing, see parts of the compound in the image below > contoured at 1 sigma level and in a 1.1 Å electron density map. > > Has anyone else experienced this? > > Best regards, > Maria > > > > Maria Håkansson, PhD, Crystallization <Screenshot 2019-02-26 at > 13.34.17.png>Facility Manager > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 > Web: www.saromics.com <http://www.saromics.com/> > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
