[phenixbb] Difficult dataset and refinement--P422? I422?Twinning?

Mon May 7 10:08:41 PDT 2012

Hi Kelly and Nat,

Thanks for your quick reply. The two space groups come out depending on which frames I started to index. Actually, in the P422 xtriage outpout, it stated it could be I422 with C'=C/3:
____________________________________________
The full list of Patterson peaks is: 

  x      y      z            height   p-value(height)
( 0.500, 0.500, 0.165 ) :   78.635   (6.634e-07)
( 0.000, 0.000, 0.330 ) :   56.292   (2.795e-05)
( 0.500, 0.500, 0.497 ) :   30.920   (1.207e-03)
( 0.500, 0.500, 0.187 ) :    4.873   (9.347e-01)

 If the observed pseudo translationals are crystallographic
 the following spacegroups and unit cells are possible: 

 space group                operator         unit cell of reference setting  
    I 4 2 2 (a,b,3*c)   x+1/2, y+1/2, z+1/6  (191.70, 191.70, 103.68,  90.00, 90.00, 90.00)
____________________________________________________________________

When I indexed as I422, some of the spots were not picked, but scaled data went to 2.65 A; P422 could cover all the spots, but resolution could only reach ~2.9A, however,  I did see 5 sigma spots around 2.6/2.7. This might indicate I have a "perfectly" split crystal so that those spots looked like they belong to a P4 space group were actually from other crystals.

Regards,

Tongqing

Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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-----Original Message-----
From: Kelly Daughtry [mailto:kddaught at bu.edu] 
Sent: Monday, May 07, 2012 12:50 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Difficult dataset and refinement--P422? I422?Twinning?

I agree.

The fact that two "crystals forms" appear, with related unit cells:
P422 data:
      unit_cell = 191.6999969 191.6999969 311.0539856 90 90 90
      space_group = "P 4 2 2"
I422 data:
unit_cell = 191.783 191.783 103.775 90 90 90
      space_group = "I 4 2 2"

indicated to me you have mis-indexed the P422 data. It is likely I422.
Kelly
*******************************************************
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
*******************************************************

On Mon, May 7, 2012 at 12:18 PM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry <kddaught at bu.edu> wrote:
>> Looking at the P422 data, it look like you have pseudo translational symmetry.
>> Did you try processing this data as I422?
>>
>> From the P422_xtriage.log:
>>
>> The full list of Patterson peaks is:
>>
>>   x      y      z            height   p-value(height) ( 0.500, 0.500, 
>> 0.165 ) :   78.635   (6.634e-07) ( 0.000, 0.000, 0.330 ) :   56.292   
>> (2.795e-05) ( 0.500, 0.500, 0.497 ) :   30.920   (1.207e-03)
>
> One word of caution: an exceptionally high off-origin peak can mean 
> that the unit cell was measured too large, and you've integrated extra 
> reflections that are really non-existent.  (I'm not sure what the 
> threshold for this is, but 80% seems pretty large.)  Splitting and 
> various indexing artifacts can sometimes lead to this.  I'd recommend 
> running labelit.index on the images and seeing what it thinks the 
> lattice should be.
>
> -Nat
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> phenixbb at phenix-online.org
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