Hello Tang,
1) For MR, you might want to try a range of homologs, or even a stack of
overlapping homologs. A normal modes server like elNemo might also help
if it can predict the "bend" your molecule undergoes upon binding. A
long shot perhaps, but stranger things have happened. You also might be
able to find the DNA by molecular replacement.
2) radiation damage increases with photons/area, not time. So no matter
what your degrees/image you want the total shuttter-open time at the end
of the data set to be below the damage limit of interest. A little web
app I made once might help: http://bl831.als.lbl.gov/xtallife.html .
These days, there is no reason not to know how long your crystal will
last before you push "collect", and it is definitely worth knowing.
-James Holton
MAD Scientist
On 7/28/2017 12:21 AM, Tang Chenjun wrote:
> Hi,
>
> Thanks to all who gave me suggestions concerning the weird diffraction pattern and I really appreciate it that Kay Diederichs help me processing my data set and answer my questions. Although the data set can be processed using HKL3000, XDS without problems, the Rwork/Rfree values are still above 0.5 after molecular replacement. There can be several reasons.
> 1) The structure change a lot after binding DNA, so it is not possible to find a solution using molecular replacement.
> 2) Strong radiation damage and 1.0 degree image widths prevent good integration results. It may be better to use 0.1 degree image widths.
> 3) Streaky spots appearing in certain directions because of anisotropy or lattice translocation disorder, or one very large unit cell dimension lying along the X-ray beam may also have an affect on data processing.
>
> Now I am optimizing the crystals to address these problems.
>
> Best wishes and thanks again for your help,
>
> Chenjun Tang
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