[ccp4bb] AW: [ccp4bb] on space group

[Herman . Schreuder]

Dear Smith,

I think your question was clear, and the answer you got was clear as well.

However, I think the question you asked was not the right question. You want to 
use a particular phrase to describe your crystal packing and you want the 
CCP4BB to endorse this. When the answer was negative, you asked again the same 
question.

The real question, in my eyes, is “What is the best way to describe my P65 
crystal packing” since I guess you want to use this in your paper. Here I would 
use something like “in the crystal, the subunits are related by a 6-fold screw 
axis”. To be more precise, you could even mention a 65-screw axis. Other board 
members may even have better descriptions.

By the way, 61, 62, 63, 64 and 65 axes are all 6-fold screw axes, but of 
different types.

Best,
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Lee
Gesendet: Donnerstag, 19. Januar 2017 06:22
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] on space group

Dear All,

Here may I make my question much clear? For the space group P 65 crystal, it 
seems we can call it "6-fold packing of subunits around a screw axis in the 
crystal". Then for the space group P 64 crystal, can it also be called "6-fold 
packing of subunits around a screw axis in the crystal"?

Smith

On Thursday, January 19, 2017 11:50 AM, Ethan Merritt 
> wrote:

On Thursday, 19 January 2017 02:33:14 AM you wrote:

>
> Dear All,
> In the literature, somebody call space group P65 crystal as  "six fold screw 
> axis crystal packing", then I would not make any mistake if I call P64 space 
> group crystal also as  "six fold screw axis crystal packing",am I right?
> I am looking forward to getting a reply from you.
> Smith


"six-fold screw axis" refers to the symmetry.

"crystal packing" refers to the molecule-to-molecule contacts regardless of 
symmetry.

So no, I don't think "six fold screw axis crystal packing" makes any sense.

--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742

[ccp4bb] AW: [ccp4bb] Wrong Space Group?

[Herman . Schreuder]

Dear Bonsor,

I fully second James suggestions but have a few additional comments:
If you get a solution in P6522 with one molecule, you should get the same 
solution in P65 with 2 molecules. One of the crystallographic symmetry 
operators would then be non-crystallographic.
The current version of Refmac will test all possible twinning operations, so 
there is no need to do it yourself (provided of course that you get a molecular 
replacement solution). 
I would also try your rebuilt model with extended helix as a model for MR. 
I suspect that the dimer which has formed is asymmetric and that it may be 
randomly packed in your crystal. If the helix is a small compared to the 
complete protein, it may not show up in twinning tests.

Good luck!
Herman 



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von James 
Holton
Gesendet: Sonntag, 15. Dezember 2013 23:29
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Wrong Space Group?

Its possible you are in a lower space group, perhaps with some twinning, but 
your search model is different enough to only find a solution when things are 
over-merged.

Try refining your P6522 model against data merged in P65. If the other copy 
(symmetry mate in P6522) does not show up, you may be in trouble (wrong MR 
solution). I'd also try refinement/building in the other triogonal/hexagonal 
space groups, but again, start with the PDB file that you got for P6522.  Just 
change the space group in the header, and switch out the MTZ file. You will 
need to merge your data in each space group and also check the a-b flip 
re-indexing for most of them. Have a look at the CCP4 reindexing list for the 
h,k,l operators to try:
http://www.ccp4.ac.uk/html/reindexing.html
note how similar they are to the twinning operators:
http://www.ccp4.ac.uk/html/twinning.html
If I have counted right, that means you have 36 jobs to run.
  
  I'd also recommend turning the TWIN option in refmac off and on for each of 
these cases. This will always give you a lower R factor, because of the dynamic 
range compression you get with twinning, but if one particular combination of 
twinning with a particular space group and axis reindexing is markedly better 
than all the others, then you have just found your right space group.  So, now 
we are up to 72 jobs, but hardly a lot of work compared to growing the crystals 
in the first place.

You might also want to try being clever and generating the symmetry mates of 
your P6522 model and refine these partners as separate molecules as you reduce 
the symmetry of the data.  It's tricky, but think of it as an exercise.  Which 
real-space operator becomes what reciprocal-space operator?  You can check your 
answer by loading it up in coot and seeing if symmetry mates clash with the 
input coordinates.

Yes, its a lot of work to try all these combinations, but that's the annoying 
thing about twinning, it opens up a lot of ambiguities.

Good luck!

-James Holton
MAD Scientist

On 12/14/2013 6:44 AM, D Bonsor wrote:
 Dear all,

 I have collected ~160 degrees of data on a new crystal form of a protein 
 which has already been solved. Data was processed with XDS and reindex, 
 scaled and truncated with Aimless. Both XDS and Pointless suggested a Laue 
 group of  P6/mmm with a possible space group of P6122 or P6522. Stats showed 
 an overall Rmerge of 0.131 but an Rpim of 0.041 (multiplicity/redundancy of 
 19.1), a completeness of 99.1% and resolution of 2.8Ang.

 With cell dimensions of 63.1 63.1 243, only one protein chain can be found in 
 the asymmetric unit (two copies would leave a solvent content of 8%). I ran 
 phaser with all alternative space groups and a single solution in P6522 with 
 a TFZ of 10.0.

 I then performed 20 Refmac cycles ending up with an R/Rfree of 35.5/45.5. I 
 open the structure and map in Coot and could see that there was a large 
 conformational change of helix-turn-helix actually becoming just a long helix 
 (https://www.dropbox.com/s/4s6g8apatsi5xcg/Before_Building.png) and then 
 dimerizing through the long helix with one of the symmetry mates.

 This section was rebuilt 
 (https://www.dropbox.com/s/5j7tv0i5yq3mxxx/After_Building.png) and ran 
 through Refmac again resulting in an R/Rfree of 35.5/44.3. Looking through 
 the rest of the structure I see nothing else really to be modeled. Nothing 
 that could bring the Rfactors down to a reasonable range.

 I have therefore tried several things. I ran the structure through Zanuda 
 server to look at other space group possibilities. The server suggested I was 
 in the correct space group. However I did reprocess the data to P6, P3, P312, 
 P321, C2221, P2 and C2, and reran phaser in search all alternative space 
 groups using the original search model but found no solutions. I did 
 reprocess the data in P1, though I did not collect enough data.

 Twinning tests show no twinning. Although that does not mean there is no 
 twinning, I can