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

[Eleanor Dodson]

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 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 good but
> it appears to be a cacodylate with five molecules in the asymmetric unit
> and an unknown cation (K gave the best results). I could not find the
> structure in the COD. I will send you the atom coordinates in a separate
> file but the data would never get through CIFCheck (which you would need
> to publish it in Acta E.).
>
> Best wishes, George
>
>
> On 20.04.2018 15:30, Rafal Dolot wrote:
>
>> Dear CCP4BB,
>>
>> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
>> DIALS gave me similar solution - 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-tetraplex
>> formation. Data were collected to almost 1 A, so it should be enough for
>> trials with direct methods/ab initio solution. What I should do first to
>> find correct SG and/or cell parameters?
>>
>> Best regards,
>>
>> Rafal
>>
>
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goetti
> ngen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-33021 or -33068
> Fax. +49-551-39-22582
>

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

[George Sheldrick]

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 good but
it appears to be a cacodylate with five molecules in the asymmetric unit
and an unknown cation (K gave the best results). I could not find the
structure in the COD. I will send you the atom coordinates in a separate
file but the data would never get through CIFCheck (which you would need
to publish it in Acta E.).

Best wishes, George


On 20.04.2018 15:30, Rafal Dolot wrote:

Dear CCP4BB,

I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, 
and DIALS gave me similar solution - 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-tetraplex formation. Data were collected to almost 1 A, so it should 
be enough for trials with direct methods/ab initio solution. What I 
should do first to find correct SG and/or cell parameters?


Best regards,

Rafal


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

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

[Harry Powell]

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 some images, with short distances between them, so for me it can 
> suggests much longer cell dimension in one direction. Maybe there is an 
> explanation. But when I tried add some spots manually, usually iMOSFLM 
> couldn't estimate cell parameters…

If XDS and iMosflm are giving you the same cell (within a small error), but you 
can see regularly spaced spots between the predictions, then the cell found by 
indexing is probably smaller than the real cell. Even if that isn’t true, it 
would be useful for an expert to have a look at the raw data so they can give 
you a diagnosis.

If I were you, at this point I would ask someone with more experience in 
processing data (perhaps the author of your favourite program (mine’s 
Mosflm….)) if they could have a look at a sample of your images to see if they 
can process the data in a way that predicts the vast majority of the 
diffraction spots.

> 
> Best regards,
> 
> Rafal
> 
> ---
> |--|
> |Rafal Dolot, Ph.D.|
> |  |
> |Polish Academy of Sciences|
> |Centre of Molecular and Macromolecular Studies|
> |Department of Bioorganic Chemistry|
> |Macromolecular Crystallography Team   |
> |Sienkiewicza 112  |
> |90-363 Lodz, Poland   |
> |Phone: +48(42)6803215 |
> |Cell:  +48 502897781  |
> |--|
> 
> W dniu 2018-04-21 23:02, Phoebe A. Rice napisał(a):
>> 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 3.4A per bp (and 43A/3.4  gives 12bp) , if this 11mer was a
>> simple symmetric duplex, there could only be 2 chains, max, but I222
>> has 8 asymmetric units.
>> This handy tool gives the same answer in a more accurate manner:
>> http://csb.wfu.edu/tools/vmcalc/vm.html
>> It says that if the RNA is intact and the space group is P2, there is
>> about 56% solvent.  If the space group is really I222, the solvent
>> content would be a rather fascinating negative 75%.
>>   -Phoebe
>> On 4/20/18, 2:37 PM, "CCP4 bulletin board on behalf of Randy Read"
>>  wrote:
>>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 does not turn out to be correct…)
>>Best wishes,
>>Randy Read
>>-
>>Randy J. Read
>>Department of Haematology, University of Cambridge
>>Cambridge Institute for Medical ResearchTel: +44 1223 336500
>>Wellcome Trust/MRC Building Fax: +44 1223 336827
>>Hills Road
>>   E-mail: rj...@cam.ac.uk
>>Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
>>>
>>> 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 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-tetraplex
>>>> formation. Data were collected to almost 1 A, so it should be enough 
>> for
>>>> trials with direct methods/ab initio solution. What I should do first 
>> to
>>>> find correct SG and/or cell parameters?
>>>>
>>>> Best regards,
>>>>
>>>> Rafal
>>>
>>> --
>>> --
>>> Paul Scherrer Institut
>>> Tim Gruene
>>> - persoenlich -
>>> OSUA/204
>>> CH-5232 Villigen PSI
>>> phone: +41 (0)56 310 5297
>>>
>>> GPG Key ID = A46BEE1A

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

[Rafal Dolot]

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 formed by one, two, or four molecules,
- crystals was obtained after long time (almost three years, now I will 
try to reduce this time) from conditions contained CaCl2, PEG400, with 
addition of spermine. Crystals are long, thin needles. I collected two 
useful datasets:
   1) 200 x 0.5 deg, above 1.00A, processed in I222/I212121 with cell 
dim. (20.64, 22.95, 43.36, 90, 90, 90)
   2) 720 x 0.5 deg, 1.10A, but only first 640 img are useful, the rest 
are blank.
I tried reprocess data to other proposed lower symmetry SG: C2 and P1, 
but I observed that Rmeas goes strongly up, with cut-off of useful 
resolution and completeness,
- there is no evidence of twinning, but tNCS is present. Output from 
phenix.xtriage is below:

  Frac. coord.  :0.0000.5000.000
  Distance to origin:   11.475
  Height relative to origin :   52.460 %
  p_value(height)   :4.848e-05
- I tried shelxt on this I222 dataset - obtained SG is Ibca as output
- 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 some images, with short distances between 
them, so for me it can suggests much longer cell dimension in one 
direction. Maybe there is an explanation. But when I tried add some 
spots manually, usually iMOSFLM couldn't estimate cell parameters...


Best regards,

Rafal

---
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Department of Bioorganic Chemistry|
|Macromolecular Crystallography Team   |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803215 |
|Cell:  +48 502897781  |
|--|

W dniu 2018-04-21 23:02, Phoebe A. Rice napisał(a):

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 3.4A per bp (and 43A/3.4  gives 12bp) , if this 11mer was a
simple symmetric duplex, there could only be 2 chains, max, but I222
has 8 asymmetric units.

This handy tool gives the same answer in a more accurate manner:
http://csb.wfu.edu/tools/vmcalc/vm.html
It says that if the RNA is intact and the space group is P2, there is
about 56% solvent.  If the space group is really I222, the solvent
content would be a rather fascinating negative 75%.

   -Phoebe

On 4/20/18, 2:37 PM, "CCP4 bulletin board on behalf of Randy Read"
 wrote:

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 does not turn out to be correct…)

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 
336827

Hills Road
   E-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk

> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
>
> 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 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-tetraplex
>> formation. Data were collected to almost 1 A, so it should be 
enough for
>> trials with direct methods/ab initio solution. What I should do 
first to

>> find correct SG and/or cell parameters?
>>
>> Best regards,
>>
>> Rafal

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

[Phoebe A. Rice]

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 3.4A per bp (and 
43A/3.4  gives 12bp) , if this 11mer was a simple symmetric duplex, there could 
only be 2 chains, max, but I222 has 8 asymmetric units.   

This handy tool gives the same answer in a more accurate manner:
http://csb.wfu.edu/tools/vmcalc/vm.html
It says that if the RNA is intact and the space group is P2, there is about 56% 
solvent.  If the space group is really I222, the solvent content would be a 
rather fascinating negative 75%.

   -Phoebe

On 4/20/18, 2:37 PM, "CCP4 bulletin board on behalf of Randy Read" 
 wrote:

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 does 
not turn out to be correct…)

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road
E-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
> 
> 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 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-tetraplex
>> formation. Data were collected to almost 1 A, so it should be enough for
>> trials with direct methods/ab initio solution. What I should do first to
>> find correct SG and/or cell parameters?
>> 
>> Best regards,
>> 
>> Rafal
> 
> -- 
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
> 
> GPG Key ID = A46BEE1A

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

[Diana Tomchick]

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 because the crystal probably diffracted 
to around 1 Å resolution, but due to beam line hardware issues, I decided it 
wasn’t worth it to try to collect the higher resolution data.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Apr 20, 2018, at 2:35 PM, Randy Read  wrote:

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 does not turn out 
to be correct…)

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
>
> 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 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-tetraplex
>> formation. Data were collected to almost 1 A, so it should be enough for
>> trials with direct methods/ab initio solution. What I should do first to
>> find correct SG and/or cell parameters?
>>
>> Best regards,
>>
>> Rafal
>
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A




UT Southwestern


Medical Center



The future of medicine, today.

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

[Randy Read]

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 does not turn out 
to be correct…)

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
> 
> 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 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-tetraplex
>> formation. Data were collected to almost 1 A, so it should be enough for
>> trials with direct methods/ab initio solution. What I should do first to
>> find correct SG and/or cell parameters?
>> 
>> Best regards,
>> 
>> Rafal
> 
> -- 
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
> 
> GPG Key ID = A46BEE1A

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

[Tim Gruene]

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 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-tetraplex
> formation. Data were collected to almost 1 A, so it should be enough for
> trials with direct methods/ab initio solution. What I should do first to
> find correct SG and/or cell parameters?
> 
> Best regards,
> 
> Rafal

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


signature.asc
Description: This is a digitally signed message part.

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

[Phoebe A. Rice]

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 4/20/18, 8:31 AM, "CCP4 bulletin board on behalf of Rafal Dolot" 
 wrote:

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-tetraplex 
formation. Data were collected to almost 1 A, so it should be enough for 
trials with direct methods/ab initio solution. What I should do first to 
find correct SG and/or cell parameters?

Best regards,

Rafal
-- 
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Department of Bioorganic Chemistry|
|Macromolecular Crystallography Team   |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803215 |
|Cell:  +48 502897781  |
|--|

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

[Keller, Jacob]

Why not try direct methods on both SG options, and maybe P1 as well? Depending 
on the wavelength and multiplicity, you might also have some good anomalous 
signal from the P's.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

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-Original Message-
From: CCP4 bulletin 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 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-tetraplex formation. Data were 
collected to almost 1 A, so it should be enough for trials with direct 
methods/ab initio solution. What I should do first to find correct SG and/or 
cell parameters?

Best regards,

Rafal
-- 
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Department of Bioorganic Chemistry|
|Macromolecular Crystallography Team   |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803215 |
|Cell:  +48 502897781  |
|--|

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

[graeme.win...@diamond.ac.uk]

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 
symmetry determination routines so I would take the outcome with a pinch of 
salt, but it could be that you have something different to what you expect. 
With this resolution you could probably solve it in P1 and work out the 
symmetry a posteri. I have solved structures of DNA in the past with SHELXT but 
this was (i) small and (ii) made the computer sweat. 

Re: I222/I212121 you cannot tell the difference from systematic absences i.e. 
what POINTLESS does. 

If XSD and DIALS give a similar solution and the reflections are all 
integrated, then on the balance of probability I would guess the answer is 
correct i.e. PG 222 and body centred, but only probably - some one will always 
come up with exceptions

As someone said earlier this week - you only know the symmetry once you’ve 
refined the structure

Best wishes Graeme

> On 20 Apr 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 - 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-tetraplex formation. 
> Data were collected to almost 1 A, so it should be enough for trials with 
> direct methods/ab initio solution. What I should do first to find correct SG 
> and/or cell parameters?
> 
> Best regards,
> 
> Rafal
> -- 
> |--|
> |Rafal Dolot, Ph.D.|
> |  |
> |Polish Academy of Sciences|
> |Centre of Molecular and Macromolecular Studies|
> |Department of Bioorganic Chemistry|
> |Macromolecular Crystallography Team   |
> |Sienkiewicza 112  |
> |90-363 Lodz, Poland   |
> |Phone: +48(42)6803215 |
> |Cell:  +48 502897781  |
> |--|


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

[Eleanor Dodson]

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 - 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-tetraplex
> formation. Data were collected to almost 1 A, so it should be enough for
> trials with direct methods/ab initio solution. What I should do first to
> find correct SG and/or cell parameters?
>
> Best regards,
>
> Rafal
> --
> |--|
> |Rafal Dolot, Ph.D.|
> |  |
> |Polish Academy of Sciences|
> |Centre of Molecular and Macromolecular Studies|
> |Department of Bioorganic Chemistry|
> |Macromolecular Crystallography Team   |
> |Sienkiewicza 112  |
> |90-363 Lodz, Poland   |
> |Phone: +48(42)6803215 |
> |Cell:  +48 502897781  |
> |--|
>

[ccp4bb] According correct space group assignment...

[Rafal Dolot]

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-tetraplex 
formation. Data were collected to almost 1 A, so it should be enough for 
trials with direct methods/ab initio solution. What I should do first to 
find correct SG and/or cell parameters?


Best regards,

Rafal
--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Department of Bioorganic Chemistry|
|Macromolecular Crystallography Team   |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803215 |
|Cell:  +48 502897781  |
|--|