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

Kelly Daughtry kddaught at bu.edu
Mon May 7 09:50:09 PDT 2012


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
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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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