Is this another example of crystallising the reagent and not the desired
material? No wonder molecular replacement failed with a DNA search model .
Eleanor
On 25 April 2018 at 20:06, George Sheldrick
wrote:
> Dear Rafal et al,
>
> With some help from Kay I think that I could find out what is ha
Dear Rafal et al,
With some help from Kay I think that I could find out what is happening
here. SHELXT finds the space group Ibca and solves the structure easily
with default parameters but has difficulty in assigning the elements
because it was not expecting arsenic (!). The data are not very go
Hi Rafal
I think this is very important -
> - I back to images. I tried to index it again under iMOSFLM. Of course, the
> most probably solutions are identical with those from XDS, but predictions
> don't cover all spots on images. In addition I observed two or three spots in
> the line on so
Dear all,
Thank you for your response.
I think, Phoebe is right. I should add some more information, maybe it
will be useful:
- the molecule of interest is a single DNA strand 11mer with sequence
5'-GGTGTGG-3', what theoretically can formed G-tetraplex, but this
kind of structure can be fo
Sadly Rafal is right the unit cell dimensions don't make sense - either the
space group is wrong or the contents have been digested before crystallization.
The size of the overall unit cell is ~21 x 23 x 43. Given a (DNA-centric but
close enough) view that a duplex is ~25A wide and there are 3.4
Several years ago I solved a small RNA structure by direct methods using the
CCP4 program ACORN, and built the model using Nautilus. This was with data to
only 1.25 Å resolution, collected at the Se edge, so there was no significant
anomalous signal.
I think that this worked like a charm becaus
I think that starting with a direct methods program like shelxt would be fun.
If that doesn’t work, it could be interesting to try to solve it by molecular
replacement with fragments varying from a tetraplex, a base pair or even just
single bases. (Assuming that Phoebe’s concern about twinning
Dear Rafal,
shelxt does not require the space group, it only needs the Laue group. If it
finds a decent solution, it'll find also the space group for you.
Best,
Tim
On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote:
> Dear CCP4BB,
>
> I've recently collected data for 11mer build of D
How do your twinning statistics look? It could be that the real space group
has lower symmetry (and thus more space for your G4 DNA).
~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/
On 4/
board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rafal
Dolot
Sent: Friday, April 20, 2018 9:31 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] According correct space group assignment...
Dear CCP4BB,
I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and DIALS
gave me simila
Rafal,
Unit cell parameters: if you look at the images, and all the reflections are
integrated, you should see little blue boxes & no missed reflections - if this
is correct then the P1 unit cell is probably correct
Regarding the space group: for this case you may find NCS confusing the
symmet
I guess do molecular replacement in both spacegroups?
Presumably the crystallographic 2-fold will create a dimer?
Eleanor
On 20 April 2018 at 14:30, Rafal Dolot wrote:
> Dear CCP4BB,
>
> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
> DIALS gave me similar solution - S
Dear CCP4BB,
I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell
dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this
size of the molecule. 11mer is rich in G, so we expect the G-tetrapl
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