[phenixbb] phaser MR
sbiswas2 at ncsu.edu
sbiswas2 at ncsu.edu
Fri Jul 24 08:15:21 PDT 2009
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
>>>>
>>>> _______________________________________________
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>>>
>>> ---------------------------------------------
>>> Francis Reyes M.Sc.
>>> 215 UCB
>>> University of Colorado at Boulder
>>>
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>>
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>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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