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

Bosch, Juergen jubosch at jhsph.edu
Tue May 8 08:24:38 PDT 2012


To what does the twin fraction refine to ? If it's close to 50% I suspect you have too low symmetry and should use the higher symmetry space group.
What's wrong with I422 and 27/32 when you have 2.7 Å data ?

Jürgen

On May 8, 2012, at 11:11 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:

Hi Jürgen, Kelly and Nat,

I tried XDS and MosFilm, they simply cannot index the data.

I reprocessed the data yesterday with HKL2000 starting from  frame #30 (splitting 1-29, 30-360), I did get it indexed to I4 and refined to very nice x/y chi^2 and covering most spots, I then used the index/refinement numbers for the whole data set. it seems that other spots were from a “nicely” positioned secondary crystal which fooled the program to pick P4 space group.

I scaled the data as I4 and I422 to see which one is better. The I4 data set, ~95% complete overall, 9.2% R-sym. Xtriage suggested it should have higher symmetry I422 or twin (-k, -h, -l, almost 50%). MR sent well and best SG is I4, 2 mol/ASU, r  and r-free went to about 27% and 32%, but if I used the twin-law in phenix.refine and ask phenix to generate r-free-flags with twinning in mind, the numbers went to ~22%  and 27%.

Shell Lower Upper Average      Average     Norm. Linear Square
limit    Angstrom       I   error   stat. Chi**2  R-fac  R-fac
      50.00   7.32   440.7     8.8     5.1  1.481  0.027  0.030
       7.32   5.81   167.2     4.2     3.2  1.868  0.045  0.048
       5.81   5.08   196.3     5.1     3.9  2.130  0.053  0.058
       5.08   4.62   243.1     6.2     4.7  2.264  0.056  0.061
       4.62   4.29   236.7     6.4     4.9  2.057  0.055  0.055
       4.29   4.03   167.6     5.6     4.7  1.819  0.067  0.066
       4.03   3.83   139.5     5.6     5.0  1.740  0.083  0.075
       3.83   3.66   110.2     5.5     5.1  1.645  0.102  0.091
       3.66   3.52    92.5     5.6     5.3  1.459  0.117  0.101
       3.52   3.40    76.5     5.7     5.4  1.372  0.143  0.124
       3.40   3.30    59.3     5.7     5.5  1.278  0.179  0.146
       3.30   3.20    47.3     5.7     5.6  1.161  0.212  0.179
       3.20   3.12    40.7     5.8     5.7  1.103  0.241  0.201
       3.12   3.04    31.6     5.8     5.8  1.057  0.298  0.254
       3.04   2.97    28.9     5.9     5.9  1.031  0.331  0.271
       2.97   2.91    22.6     5.9     5.9  0.985  0.400  0.340
       2.91   2.85    19.0     6.0     6.0  0.991  0.484  0.405
       2.85   2.80    17.1     6.1     6.1  0.957  0.518  0.437
       2.80   2.75    14.6     6.2     6.2  0.908  0.577  0.485
       2.75   2.70    13.0     6.4     6.3  0.931  0.645  0.550
  All reflections    112.9     5.9     5.3  1.455  0.092  0.066

The I422 data (below), 1 mol/ASU, r and r-free were about 27% and 32%.

Shell Lower Upper Average      Average     Norm. Linear Square
limit    Angstrom       I   error   stat. Chi**2  R-fac  R-fac
      50.00   7.32   430.0     8.4     5.0  1.344  0.025  0.028
       7.32   5.81   163.4     4.0     3.0  1.489  0.040  0.042
       5.81   5.08   192.4     4.8     3.6  1.694  0.046  0.052
       5.08   4.62   231.6     5.6     4.3  1.790  0.049  0.053
       4.62   4.29   227.8     5.8     4.5  1.534  0.045  0.043
       4.29   4.03   161.3     5.0     4.2  1.401  0.055  0.052
       4.03   3.83   135.3     5.0     4.4  1.367  0.066  0.059
       3.83   3.66   106.2     4.9     4.4  1.302  0.082  0.071
       3.66   3.52    88.1     4.8     4.5  1.253  0.097  0.082
       3.52   3.40    75.0     4.9     4.6  1.193  0.113  0.096
       3.40   3.30    56.7     4.8     4.6  1.121  0.144  0.115
       3.30   3.20    44.8     4.8     4.7  1.061  0.172  0.141
       3.20   3.12    38.0     4.8     4.7  1.011  0.203  0.166
       3.12   3.04    29.1     4.7     4.7  1.029  0.253  0.209
       3.04   2.97    27.7     4.8     4.8  0.985  0.261  0.209
       2.97   2.91    21.4     4.9     4.8  0.917  0.320  0.266
       2.91   2.85    18.3     4.9     4.8  0.949  0.380  0.316
       2.85   2.80    16.1     4.9     4.9  0.955  0.431  0.358
       2.80   2.75    14.2     5.0     5.0  0.940  0.483  0.399
       2.75   2.70    12.6     5.2     5.2  0.886  0.536  0.462
  All reflections    110.9     5.1     4.5  1.236  0.076  0.054


So my questions are:

1.    Is it really twinned since including twin-law in refinment gave much better numbers?
2.    When refining with twin-law, Are the maps by phenix.refine output already “corrected” mtz/map?
3.    If I use xray_data.r_free_flags.generate=True, can I write the data mtz out with the generated r-free-flags so that each round of refinement uses the same CV set?

Thnaks,



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)
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From: Bosch, Juergen [mailto:jubosch at jhsph.edu]
Sent: Monday, May 07, 2012 1:34 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Difficult dataset and refinement--P422? I422?Twinning?

Why don't you index over the whole dataset (XDS) ?
Or at least over a couple of images (Mosflm)

Jürgen

On May 7, 2012, at 12:50 PM, Kelly Daughtry wrote:


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
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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<mailto:nechols at lbl.gov>> wrote:

On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry <kddaught at bu.edu<mailto: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?


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