Dear Chen,
I will answer with some question :
- How is the refinement going ? Is the RNA properly taking in count ?
Which soft do you use ?
- How do you solve the structure ? MR ? If it's MR did you use a model
which contain both protein and RNA ? Did you try to solve with the
protein only ? Maybe you are "forging" RNA.
- Depending of your data (wavelenght and redundancy) you can try to
calculate an anomalous difference map to see the phosphorus of the RNA
to be more confident.
- Last point, it could be the occupancy connected with the stability of
the complex, maybe sometimes RNA is here sometimes not. I see that one
time with two complex in the same ASU, one has one missing partner.
For my side, I really like to refine my DNA-protein complex with Buster
from global Phasing. It gives you a very nice and informative density
map. If you have this possibility let's try.
Hope to help.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 21/06/2017 09:34, Chen WeiFei wrote:
Dear All,
We have get a complex crystal and the resolution can be refined to
nearly 1.84 Å. But the electron density of the RNA is very weak.
In some datasets we can't find any density of the RNA and in other
datasets we can see more or less some RNA density.
For now we can build 6-7 nucleotides but we can't distinguish the
rigth sequence.
If anyone has the same problem and how to solve this problem.
Best Regards,
Dr Wei-Fei Chen
College of Life Sciences,
Northwest A&F University
