>We have a specific case with a 24 kDa protein crystallizing in P6522 >with resolution of 2.5 - 3 A, which should be comparable to most >cases. The ligands have 10 - 20 non-hydrogen atoms (most of the time >we don't know, we are actually screening for them). How far should >we refine to see if we have only water molecules or a ligand bound >- to an Rfree of 0.45 or 0.40 or 0.35? >greetings > Gottfried
In my opinion, this is not easy to reduce to a single number since there are too many variables. True resolution and quality of the data, the actual non-isomorphism (and in particular conformational changes), B-factor of the ligand, etc. The coy answer would be "enough refinement to convince yourself that it is or isn't there", but in all seriousness, it does boil down to a judgment call on when you have reached the point of diminishing returns. I think the problem is particularly complex with the fragment screening work you describe, since you may or may not know where the ligands are actually binding. Tricky stuff indeed. Steve ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ------------------------------------------------------------------------------
