My first guess was also a metal ion. However, a tryptophan as Fred suggested cannot be ruled out. A simple preliminary test is to scroll up the contouring level and look when the contours of the blob disappear. If the contours quickly disappear, you have something disordered or light. If the contours of the blob disappear at the same moment or later as e.g. sulfur atoms, you have something heavy like a metal ion. You still have to fit all possibilities and see what refines best.
Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Matthias Zebisch Gesendet: Dienstag, 10. Dezember 2013 14:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Fwd: undefined edensity blob at glutamine sidechain check an anomalous map! The obvious thing to do to rule out gold binding ----------------------------------------- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk<mailto:matth...@strubi.ox.ac.uk> Website http://www.strubi.ox.ac.uk ----------------------------------------- On 12/10/2013 12:44 PM, PriyankMaindola wrote: dear members i am trying to solve this crystal structure but I am puzzled with an undefined blob that appeared at a glutamine residue after refinement. I have attached pics of that below. Is it a covalent modification of acid-amide side chain.. ... as there is no charged environment around and density seems continuous. please suggest .... following reagents were encountered by protein during purification, crystallization and soaking : phenyl methyl sulfonyl fluoride benzamidine tris dtt (could it be cyclized dtt?) k[au(cn)2] acidic pH isopropanol citrate sulfate phosfate K+, Na+, Cl- map contour: 2fo-fc: 1rmsd fo-fc (green): 3 rmsd -- Priyank
