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 <[log in to unmask]> 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 <[log in to unmask]>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
>
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