Dear Colin, I think the residual blob usually represents a combination of different chemical entities.
I think the correct thing to do is to try to dock all the possible chemical entities you have in your crystallisation buffer, purification buffers and things that have carried through in an unknown manner from the purification into the blob and try and estimate their occupancies (if they give a chemically reasonable fit). If it is a big enough blob you could just try and dock glycerol (if this is in your cryo) and water and have them at half occupancy, and have a comment in the pdb header. Regards, Ben Ben Bax Senior Scientific Investigator BioMolecular Sciences UK RD Platform Technology & Science GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK Email benjamin.d....@gsk.com<mailto:benjamin.d....@gsk.com> Mobile +44 (0) 7912 600604 Tel +44 (0) 1438 55 1156 gsk.com<http://www.gsk.com/> | Twitter<http://twitter.com/GSK> | YouTube<http://www.youtube.com/user/gskvision> | Facebook<http://www.facebook.com/glaxosmithkline> | Flickr<http://www.flickr.com/photos/glaxosmithkline> [cid:image001.png@01D0A754.53FEE6D0] From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Levy Sent: 14 June 2015 09:53 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Residual density feature Dear all, I am currently working on a structure that contains a residual density feature located within the active site. Due to a combination of factors including limited occupancy, modest resolution, twinning etc it has not been possible to unambiguously identify this feature despite fairly extensive efforts. What is the best way of dealing with such a feature when depositing the structure? Ideally I would like to draw attention to the presence of residual density whilst not implying that I have been able to identify it. Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.l...@manchester.ac.uk<mailto:c.l...@manchester.ac.uk> ________________________________ This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS.
