[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.
>>>>> Any advice is appreciated,
>>>>> Shya
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>> ---------------------------------------------
>>>> Francis Reyes M.Sc.
>>>> 215 UCB
>>>> University of Colorado at Boulder
>>>>
>>>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>>>
>>>> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
More information about the phenixbb
mailing list