Structures of a protein-ligand complex are often determined without the need of running a molecular replacement program: a difference Fourier is generated to locate the ligand, usually after a few rounds of rigid bodies and / or atom positional refinement..
They may account for many of the 19,000 unaccounted structures. There is not a full consensus on what Molecular Replacement mean. Some consider a structure determined by simple Fourier difference maps as a case of Molecular Replacement where the solution is identity (or close to identity). Others (like me) think the terms of "solved by Molecular Replacement" should be reserved to cases where the non-isomorphism between the original structure and the one to solve is beyond the radius of convergence of refinement and reaching the solution requires the use of a Molecular Replacement program (precisely). The point is that it's unclear whether you can truly get the statistics you want if there is no universal definition for the terms used. Thierry From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Raji Edayathumangalam Sent: Monday, April 15, 2013 9:48 AM To: [email protected] Subject: [ccp4bb] Off-topic: PDB statistics Hi Folks, Does anyone know of an accurate way to mine the PDB for what percent of total X-ray structures deposited as on date were done using molecular replacement? I got hold of a pie chart for the same from my Google search for 2006 but I'd like to get hold of the most current statistics, if possible. The PDB has all kinds of statistics but not one with numbers or precent of X-ray structures deposited sorted by various phasing types or X-ray structure determination methods. For example, an "Advanced Search" on the PDB site pulls up the following: Total current structures by X-ray: 78960 48666 by MR 5139 by MAD 5672 by SAD 1172 by MIR 94 by MIR (when the word is completely spelled out) 75 by SIR 5 by SIR (when the word is completely spelled out) That leaves about 19,000 X-ray structures either solved by other phasing methods (seems unlikely) or somehow unaccounted for in the way I am searching. Maybe the way I am doing the searches is no good. Does someone have a better way to do this? Thanks much. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University 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 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.
