Here is some more info on the data: lowest res. shell (50-8.0A): Rsym=4.4%, I/sig=100. detector ADSC315, 1 degree oscillations, mosaicity around 0.3
The Rsym stays high whether I merge just the first 30 frames or 200 frames. Wouldn't that speak against radiation damage? The crystals were grown from 2.5 M sodium formate and cryoprotected in 2.8 M sodium formate, 30% glycerol. Ursula On Mon, Oct 14, 2013 at 11:39 AM, Dominika Borek <domin...@work.swmed.edu>wrote: > There are several possibilities: > > (1) Radiation damage causes such bump in R-merge at medium resolution > (2) Crystallization in very high salt that absorbs causes such behaviour, > e.g. if your crystallized from 2M sulfate. > (3) Very short exposure time -- very short means shorter than 1 second per > image -- that results in large errors due to goniostat instability. > (4) Very short exposure may also result in errors due to shutter problems. > (5) Very weak diffraction. All errors will be "better" visible with weak > diffraction. > > Any combination of the above factors is also possible. > > What are R-merges in the lowest resolution shell i.e. 50-8 A? If they are > high too -- this is probably goniostat, shutter or beam instability. If > they are low in the lowest resolution shell -- this probably radiation > damage. > > What is the mosaicity? Low means lower than 1 degree for some people, for > others less than 0.1 degree? > > What detector was used to collect data? Oscillation step? What is I/s(I) > in the lowest resolution shell? > > Dominika > > > Ursula Schulze-Gahmen wrote: > > I have a data set with high Rsym in the lower resolution ranges, and I > > don't understand what is going on. > > > > The crystal diffracts to about 3.0 A and has large cell dimension ( space > > group P6522 a= 185., c= 360.) Mosaicity is low. I processed the data in > > P6522, solved the structure and refined it. The maps look good and the > > structure refines very well to R/Rfree of 20.5, 23.5%. > > > > But the dataset has a total Rsym of 22%, a redundancy of 20, an Rpim of > > 7.6%, and CC1/2 of 0.55 in the highest resolution shell. > > The problem seems to be in the lower resolution region around 8-5.5A. The > > Rsym there is around 20%, it actually has a bump in this resolution > region > > and is slightly lower at 5.0 A before it steadily increases to higher > > resolution. The high Rsym region between 8-5.5 A correlates with very low > > I/sig which also increases again around 5.0 A and then steadily > decreases. > > The diffraction image shows very weak spots too. > > > > My question is: Is it likely that the data are processed correctly and > the > > crystal packing causes this strange diffraction pattern, or is there > > something wrong with the data processing or the crystal? > > > > Any suggestions would be greatly appreciated. > > > > Ursula > > > > > Dominika Borek, Ph.D. *** UT Southwestern Medical Center > 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 > 214-645-6378 (phone) *** 214-645-6353 (fax) > > -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
