[phenixbb] P32 twin or p3221?

lauren lauren at gate.sinica.edu.tw
Thu Dec 3 04:49:03 PST 2009

Hi everyone,


I have a dimmer protein diffract to 1.6 A resolution.

After processing the data, the Linear R-fac was 0.26/0.038 (last/all), the
data quality seems good.

This data can be processed to P3 or P321 with the R-fac almost the same

After that, I used Bales to do the MR, two solutions were found in P32
(dimmer) and one in P32 21 (monomer)

Then, I refine the structure using phenix.refine in both P32 and P32 21
sets, but the R/Rfree stopped at 0.19/0.25 and never goes down.

Rfree 25% seems a little bit too high for a 1.6 resolution data.

However, if I treat the P32 data as a twin (with twin law h,-h-k,-l ), the
R/Rfree can down to 0.12/0.18.


I use P3 to run the phenix.xtriage (see bellows), it looks like the L-test
says it is not a twin data.

So, I am wondering is it a twin data or not?


The results are as follow.

"Twinning and intensity statistics summary (acentric data):


Statistics independent of twin laws

  - <I^2>/<I>^2 : 2.105

  - <F>^2/<F^2> : 0.773

  - <|E^2-1|>   : 0.757

  - <|L|>, <L^2>: 0.508, 0.344

       Multivariate Z score L-test: 2.013


Statistics depending on twin laws


| Operator  | type | R obs. | Britton alpha | H alpha | ML alpha |


| -h,-k,l   |   M  | 0.484  | -0.003        | 0.022   | 0.022    |

| h,-h-k,-l |   M  | 0.026  | 0.454         | 0.479   | 0.478    |

| -k,-h,-l  |   M  | 0.507  | -0.004        | 0.026   | 0.022    |



Patterson analyses

  - Largest peak height   : 8.386

   (corresponding p value : 0.29163)



The largest off-origin peak in the Patterson function is 8.39% of the

height of the origin peak. No significant pseudotranslation is detected.


The results of the L-test indicate that the intensity statistics

behave as expected. No twinning is suspected.

Even though no twinning is suspected, it might be worthwhile carrying out

a refinement using a dedicated twin target anyway, as twinned structures

low twin fractions are difficult to distinguish from non-twinned structures.


The correlation between the intensities related by the twin law h,-h-k,-l
with an

estimated twin fraction of 0.45 %

is most likely due to an NCS axis parallel to the twin axis. This can be
verified by

supplying calculated data as well."







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