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Re: [ccp4bb] phasing with se-met at low resolution |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: phasing with se-met at low resolution From: "Soisson, Stephen M" stephen_soisson {- at -} MERCK {- dot -} COM Date: 2009-05-10 Engin- I succesfully solved a 4.1 Ang SeMet MAD (4 wavelength) awhile ago. Please see pdb entry 1XDV Cell. 2004 Oct 29;119(3):393-405. It is hard work, but can be done. Steve ------------------------------------------------------------------------ ------ Stephen M. Soisson, Ph.D. Global Structural Biology Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax: (215) 652-9051 stephen_soisson@merck.com -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Engin Ozkan Sent: Sunday, May 10, 2009 5:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] phasing with se-met at low resolution Hi everyone, I thought I start a new thread while it is unusually quiet on the bb. I am pondering over the practical limitations to MAD and SAD phasing with Se-Met at low resolution. What is the lowest resolution at which people have solved structures "only" using phases from selenium in a "realistic" case? Let me further qualify my question: My *realistic* *low* resolution case is where 1. Rmerge over all resolution bins is 6-10% (i.e. your crystals are lousy). 2. Resolution limit is worse than 3.5 Angstroms, where / the last resolution bin is between 1 and 3 (i.e. your crystals are really lousy). 3. Assuming good selenium occupancy (~85%; I work with eukaryotic expression systems, so 100% is not usually achieavable), 4. The number of selenium atoms are enough many that the Crick-Magdoff equation would give you *at least* an average 5% change in intensities (assuming 6 electrons contributed per selenium, based on both absorptive and dispersive differences being at about 6 e- at the absorption edge). 5. and specifically, no other phases and molecular replacement solutions are available. Obviously, I have a case very similar to what's described above, and three years of failure with heavy atom derivatization (I am still trying). I would be happy to hear about Se-Met cases, and data collection strategies (2wl vs. 3wl MAD vs. SAD, etc.) and phasing methods used in these cases, or references of them. Again, no other partial phases, and no data cut off at 3.6 A with an I/s of 15 in the last resolution bin. Are there any examples out there? Searching the RCSB and PubMed did not point out to me many successful cases. Thanks, Engin P.S. I would also appreciate the specific query type for searching the PDB on the web for phasing method (MR, MAD, SAD, MIR, etc.). They seem to have everything under the sun searchable, but I cannot find this one. 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. CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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