[phenixbb] P32 twin or p3221?

[lauren]

Hi Peter,

 

Thanks for your reply.

 

>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.

>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.

 

>Do an R vs R analysis by loading up a model as well in xtriage to get a
clue about the extend of the pseudo symmetry.

 

I do the R vs R analysis with P32 in xtriage, but the R value seems very
close to zero.

And the D_ncs is high (0.95) in resolution range 9.9841-4.2623, which may
indicate an incorrect point group?

 

 

The results are as follow.

 

---------------------------------------------

 Analysing possible twin law :  h,-h-k,-l

---------------------------------------------

 

mean |H| : 0.018   (0.50: untwinned; 0.0: 50% twinned)

mean H^2 : 0.001   (0.33: untwinned; 0.0: 50% twinned)

Estimation of twin fraction via mean |H|: 0.482

Estimation of twin fraction via cum. dist. of H: 0.487

 

Britton analyses

 

  Extrapolation performed on  0.47 < alpha < 0.495

  Estimated twin fraction: 0.455

  Correlation: 0.9777

 

R vs R statistic:

  R_abs_twin = <|I1-I2|>/<|I1+I2|>

  Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

 

   R_abs_twin observed data   : 0.022

   R_abs_twin calculated data : 0.090

 

  R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>

   R_sq_twin observed data    : 0.001

   R_sq_twin calculated data  : 0.006

Perfoming correlation analyses

  The supplied calculated data are normalized and artificially twinned

  Subsequently a correlation with the observed data is computed.

   Results:

     Correlation :  0.832594802609

     Estimated twin fraction :  0.49

Maximum Likelihood twin fraction determination

    Zwart, Read, Grosse-Kunstleve & Adams, to be published.

   The estimated twin fraction is equal to 0.478

  Log[likelihood]:       78991.418

  twin fraction: 0.443

  D_ncs in resolution ranges:

     9.9841 -- 4.2623 :: 0.950

     4.2623 -- 3.4280 :: 0.694

     3.4280 -- 3.0083 :: 0.655

     3.0083 -- 2.7394 :: 0.885

     2.7394 -- 2.5466 :: 0.853

     2.5466 -- 2.3986 :: 0.824

     2.3986 -- 2.2800 :: 0.817

 The correlation of the calculated F^2 should be similar to

 the estimated values.

 Observed correlation between twin related, untwinned calculated F^2

 in resolutiuon ranges, as well as ewstimates D_ncs^2 values:

 Bin    d_max     d_min     CC_obs   D_ncs^2

  1)    9.9841 -- 4.2623 ::  0.981    0.902

  2)    4.2623 -- 3.4280 ::  0.970    0.482

  3)    3.4280 -- 3.0083 ::  0.958    0.429

  4)    3.0083 -- 2.7394 ::  0.954    0.783

  5)    2.7394 -- 2.5466 ::  0.964    0.728

  6)    2.5466 -- 2.3986 ::  0.953    0.679

  7)    2.3986 -- 2.2800 ::  0.963    0.667

 

Best Regards,

 

Lauren

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