[phenixbb] phaser MR

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Jul 27 08:06:02 PDT 2009

```Shya

I'm curious as to how you resolved this problem. To quote, you applied
a twin law for the P 42 22 space group? I wasn't aware that there were
twin laws for this space group? How did you determine the twin law?

Thanks

FR

On Jul 24, 2009, at 9:15 AM, sbiswas2 at ncsu.edu wrote:

> Hi,
> Thanks for your response. So I did one cycle of refinement and
> indeed the
> R work goes down by 5 points when I apply twin law at P4222 space
> group
> and when I look at the map the clashes that were present before are no
> longer there. I will try to scale it in P4 or P422 and see how it
> looks. I
> used HKL2000 to scale the data and have no idea if it will make a
> difference to use SCALA.
> This is what I got from phenix xtriage:
> These values look inbetween untwinned and perfect twin
> Acentric reflections
>   <I^2>/<I>^2    :1.980   (untwinned: 2.000; perfect twin 1.500)
>   <F>^2/<F^2>    :0.797   (untwinned: 0.785; perfect twin 0.885)
>   <|E^2 - 1|>    :0.727   (untwinned: 0.736; perfect twin 0.541)
> Centric reflections
>   <I^2>/<I>^2    :2.863   (untwinned: 3.000; perfect twin 2.000)
>   <F>^2/<F^2>    :0.673   (untwinned: 0.637; perfect twin 0.785)
>   <|E^2 - 1|>    :0.925   (untwinned: 0.968; perfect twin 0.736)
>
> -----------------------------------------------
> |  Z  | Nac_obs | Nac_theo | Nc_obs | Nc_theo |
> -----------------------------------------------
> | 0.0 |   0.000 |    0.000 |  0.000 |   0.000 |
> | 0.1 |   0.074 |    0.095 |  0.208 |   0.248 |
> | 0.2 |   0.164 |    0.181 |  0.319 |   0.345 |
> | 0.3 |   0.246 |    0.259 |  0.391 |   0.419 |
> | 0.4 |   0.322 |    0.330 |  0.452 |   0.474 |
> | 0.5 |   0.388 |    0.394 |  0.505 |   0.520 |
> | 0.6 |   0.445 |    0.451 |  0.552 |   0.561 |
> | 0.7 |   0.497 |    0.503 |  0.592 |   0.597 |
> | 0.8 |   0.541 |    0.551 |  0.630 |   0.629 |
> | 0.9 |   0.587 |    0.593 |  0.659 |   0.657 |
> | 1.0 |   0.631 |    0.632 |  0.679 |   0.683 |
> -----------------------------------------------
> | Maximum deviation acentric      :  0.021    |
> | Maximum deviation centric       :  0.040    |
> |                                             |
> | <NZ(obs)-NZ(twinned)>_acentric  : -0.009    |
> | <NZ(obs)-NZ(twinned)>_centric   : -0.014    |
>
> Thanks again for the valuable input,
>
> Shya
>
>
>
>
> Shya,
>>
>> Did phaser complain that the asymmetric unit was too full?  How do
>> the
>> self rotation maps look? Are the crystallographic peaks exact or off
>> by a few degrees (your resolution data may make it difficult to see
>> this)? How do the N(z) cumulative intensity distributions look (make
>> sure to calculate this with thin resolution bins, i.e. increase BINS
>> in Scala I think)? Does your data look sigmoidal on this plot?
>>
>> Perfect twinning or an NCS that's close to a crystallographic axis is
>> difficult to diagnose from merged intensity statistics and even more
>> difficult with resolution worse than 2.5. I recommend Dauter Acta
>> Cryst (2003) D59 2004-2016 for a good discussion of this.
>>
>> Your space group might be too high. See the subgroups of P422 at
>> http://cci.lbl.gov/~phzwart/p422_2.png
>> . Reintegrate and merge the data in each space group, MR a single
>> copy
>> of your model  (let phaser complete the ASU) and compare the Rpim's
>> (from scaling/merging) and the Rwork/Rfree from a rigid body refine
>> without NCS, with NCS, with appropriate twin laws, and with twin laws
>> + NCS. No need to do a full refinement just yet.  Allow phenix.refine
>> to create the Rfree flags. Choose the space group which gives the
>> best
>> statistics.
>>
>> I recently had a case (Hardin, Reyes, Batey J. Biol. Chem., Vol. 284,
>> Issue 22, 15317-15324, May 29, 2009) of a protein that merged into
>> P422 but was difficult to refine in that space group. I brought it
>> back to P4 and refined with NCS+twin to give more reasonable Rwork/
>> Rfree (5-7% difference from the P422 to P4).
>>
>> HTH,
>>
>> FR
>>
>>
>>
>> On Jul 23, 2009, at 3:54 PM, sbiswas2 at ncsu.edu wrote:
>>
>>> Hi Francis,
>>> Thanks for your response. The matthews coefficient suggests two
>>> molecules
>>> in the AU. Phaser also finds two molecules. I ran the dataset
>>> through
>>> phenix xtriage it did not indicate twinning though. The molecule
>>> also
>>> exists in nature as a monomer.
>>> Shya
>>>
>>>
>>>> Twinning? What's your matthews coefficient say? Do you know if your
>>>> structure is a multimer (biochemistry, etc)? Does  it agree with
>>>> the
>>>> matthews coefficient?
>>>>
>>>> If the unit cell is  not big enough to hold all of the
>>>> contents,then
>>>> this is an indicator for twinning .
>>>>
>>>> FR
>>>>
>>>> On Jul 23, 2009, at 3:09 PM, sbiswas2 at ncsu.edu wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I was trying to solve a structure by molecular replacement. I
>>>>> scaled
>>>>> the
>>>>> data in P4222 space group (resolution 2.7A) with two molecules in
>>>>> the
>>>>> assymmetric unit (molecule A and B) I ran phaser with my model and
>>>>> got a
>>>>> Zscore of 5.1. When I look at the map that I got from phaser I
>>>>> could
>>>>> easily see good electron density for both molecules, However upon
>>>>> inspection of the electron density map there were considerable
>>>>> interaction
>>>>> or clashes with molecule B and a symmetry atom. Molecule A had no
>>>>> clashes
>>>>> however with the symmetry atoms. I was wondering if anyone knows
>>>>> how
>>>>> to
>>>>> resolve this.  Could it be a problem of space group. The
>>>>> statistics
>>>>> are
>>>>> good for space group P4222 and the I/sigI was good till 2.7A.
>>>>> Shya
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
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>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>> ---------------------------------------------
>>>> Francis Reyes M.Sc.
>>>> 215 UCB
>>>> University of Colorado at Boulder
>>>>
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>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB