Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

[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 similar solution

Re: [ccp4bb] According correct space group assignment...

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

Re: [ccp4bb] According correct space group assignment...

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

[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 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