Hi Ursula, if you look at the Wilson plot, you see a minimum near 6A resolution. This means that in the range 7-5A, intensities are low, and Rsyms are therefore elevated.
best, Kay On Mon, 14 Oct 2013 11:52:03 -0700, Ursula Schulze-Gahmen <[email protected]> wrote: >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 ><[email protected]>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 >
