Dear Engin Ozkan, You have told us how bad your crystals are, but you did not mention how good your anomalous signal is: 1. To what resolution does your anomalous signal extend and what statistic is used for this estimate? 2. Do your dispersive and Bijvoet Pattersons look similar and what is the measure of similarity?
This structure http://www.pdb.org/pdb/explore/explore.do?structureId=1K28 which contains ~1100 residues in the asymmetric unit (and ~3500 in the entire complex), was solved using a chimerical SeMet derivative, in which one protein was SeMet labeled (17 Se per a.u.) and the other was native. The Semet dataset had a detectable anomalous signal to 4 A resolution (at most). The diffraction extended to 2.9A resolution. Sincerely, Petr ----------------------------------------------------------- Petr Leiman Institut de physique des systèmes biologiques École Polytechnique Fédérale de Lausanne (EPFL) Cubotron/BSP-415 CH-1015 Lausanne Switzerland > -----Original Message----- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Engin Ozkan > Sent: Sunday, May 10, 2009 11:01 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 <I>/<sigma> in > 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.
