Concerning "low resolution SAD phasing" I would like to add some information here:
1. OASIS (version 2000) helped solving the unknown structure 1u9s in phasing the 2.9A SAD data ( http://www.sciencemag.org/content/suppl/2004/09/30/306.5693.104.DC1/Krasilnikov.SOM.pdf ). 2. OASIS-2004 helped solving the unknown protein TT0570 (2d5w, with 1206 residues and 18 sulfur atoms in the AU) in phasing the 2A SAD data (Acta Cryst. (2006). D62, 891–896). In a test calculation, the same protein can be automatically solved by the program combination of ShelxD-Oasis-DM-Resolve(build only)-Buccaneer-RefMac with a truncated data set at 3.0A giving a model of about 95% of the whole structure. Even the truncated data at 4.0A can give a meaningful electron density map ( http://www.ccp4.ac.uk/schools/China-2011/talks/Oasis_Fan.pdf). 3. OASIS-2004 also helped solving the unknown protein Tom70p (2gw1, 1086 residues in the AU) in phasing the 3.3A Se-SAD data (Nature Struct. Mol. Biol. (2006) 13, 589-593). Haifu Fan On Thu, Jun 16, 2011 at 3:19 PM, George M. Sheldrick < gshe...@shelx.uni-ac.gwdg.de> wrote: > Tommi, > > Since you ask, SHELX and other 'direct methods' run out of steam at about > 1.2A and for many years very few unknown structures have been solved at > lower resolution than 1.2A. Recntly this picture was changed by the > introduction of ARCIMBOLDO, which has solved a number of structures ab > initio with 2.0-2.1A native data and no other phase information. However > ARCIMBOLDO requires at least one alpha-helix in the structure and > substantial > computer power. This is still a long way from your 6A data! > > If you are using SHELXD or other programs to locate heavy atoms from SAD, > MAD or SIRAS data much lower resolutions are possible, because the heavy > atoms are still well resolved from each other. You can think of the 1.2A > limit for native data as the requirement for resolving the atoms from each > other (for a more sophisticated explanation see Morris and Bricogne, Acta > Cryst. D59 (2003) 615-617). Nevertheless, for finding the heavy atoms at > very low resolution you need all the phase information you can get, so MAD > and SIRAS will be better than SAD, and it helps to combine phases from > several different sources. > > George > > > On Thu, Jun 16, 2011 at 09:22:42AM +0300, tommi kajander wrote: > > Hi, > > > > Thanks for all the comments, i was more wondering what the state of > > the art might > > be here, we have done similar thing at 4 Å (with 3 Å data though) 10 > > years or so back > > with SnB. Maybe we need to get a heavier atom derivative indeed the > > break the phases, > > but i'll keep banging for now.. > > > > I have tried quite a lot, and was mainly wondering what was the > > world record > > nowadays in desperate solutions by SHELX/other direct methods... > > > > playing around with XDS, data is finally quite ok to 6 Å low res > > anom CC 100-90%, > > SigAno about 3... goes down obviously but not terribly fast there is > > signal all the way to 6Å. > > > > Inverse beam data collection would probably be a good idea indeed > > next time, native or > > second wavelength or rahter both might help i assume.. > > thanks to Tim, Clemens, Poul and others for comments, > > Best, > > Tommi > > > > > > On 15.6.2011, at 17.16, Tim Gruene wrote: > > > > >Hi Tommi, > > > > > >Give it a try? > > >You give very little information, e.g. > > >- the data quality, > > >- possible radiation damage, > > >- isomorphism with a native data set, and > > >- what you have tried so far. > > > > > >If you have a native data set with an isomorphous unit cell, try > > >SIRAS instead > > >of SAD. > > > > > >Tim > > > > > >On Wed, Jun 15, 2011 at 04:36:59PM +0300, tommi kajander wrote: > > >>Dear all, > > >> > > >>Does anyone have suggestions for 6 Å resolution phasing with large > > >>number (40-50) Se sites (SAD so far)?? > > >> > > >>Thanks a bunch, > > >>Tommi > > >> > > >>Tommi Kajander, Ph.D., Docent > > >>Macromolecular X-ray Crystallography > > >>Research Program in Structural Biology and Biophysics > > >>Institute of Biotechnology > > >>P.O. Box 65 (Street: Viikinkaari 1, 4th floor) > > >>University of Helsinki > > >>FIN-00014 Helsinki, Finland > > >>Tel. +358-9-191 58903 > > >>Fax +358-9-191 59940 > > >> > > > > > >-- > > >-- > > >Tim Gruene > > >Institut fuer anorganische Chemie > > >Tammannstr. 4 > > >D-37077 Goettingen > > > > > >GPG Key ID = A46BEE1A > > > > > > > Tommi Kajander, Ph.D., Docent > > Macromolecular X-ray Crystallography > > Research Program in Structural Biology and Biophysics > > Institute of Biotechnology > > P.O. Box 65 (Street: Viikinkaari 1, 4th floor) > > University of Helsinki > > FIN-00014 Helsinki, Finland > > Tel. +358-9-191 58903 > > Fax +358-9-191 59940 > > > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 >
