Hi All, I had an interesting case recently where a Cl atom of a chlorophenyl moiety went missing in a structure (primary X-ray damage was the suspected culprit). Small molecule Mass Spec suggested the atom was there to start with but it was quite obviously missing in the maps (1.9Ang) and the des-chloro refined much better. I was asked to replace the missing atom as it was seen as misleading because all the assay and biophysical data was generated with the chlorophenyl compound; this after all, is what the X-ray model was supporting. I did wonder where the Cl atom ended up and in what state.
David Hargreaves Associate Principal Scientist _____________________________________________________________________ AstraZeneca Discovery Sciences, Structure & Biophysics Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com<mailto:name.surn...@astrazeneca.com> Please consider the environment before printing this e-mail From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 13 June 2014 10:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Invisible atoms in ligands Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx -------------------------------------------------------------------------- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
