[phenixbb] NCS and R-Values Hung up at ~0.42/0.46

[Peter Zwart]

How do the rest of the intensity statistics look?

P

On 10 July 2015 at 14:41, John Bruning <jmbruning at gmail.com> wrote:

> Hi Everyone,
> I collected two datasets of the same ligand bound structure at 2.4 and 2.1
> Å resolution. The apo structure has already been solved to 2.2Å resolution
> in P31 (and P3121 for SeMet). After processing each dataset as both P31 and
> P3121 in MOSFLM, I proceeded with MR with Phaser using sequential partial
> search models to place either 3 copies in the ASU for P3121, or 6 copies
> for P31. (The previously solved apo structure had 6 copies of the same
> protein in the ASU).
> *** in summary two datasets, processed as both P31 or P3121
>
> After running xtraige for either .mtz, I get this warning about NCS:
>
> Largest Patterson peak with length larger than 15 Angstrom:
>  Frac. coord.              :    0.333   -0.333   -0.153
>  Distance to origin        :   56.728
>  Height relative to origin :   26.388 %
>  p_value(height)           :    2.659e-03symmetry.
>
> Translational pseudo-symmetry is very likely present in these data.
> Be aware that this will change the intensity statistics and may impact
> subsequent analyses, and in practice may lead to higher R-factors in
> refinement.
> ​Regardless, I can proceed with the MR using sequential partial search
> models to place either 3 copies (P3121) or 6 copies (P31) with decent
> solutions (i.e. packing looks good upon inspection, scoring looks
> appropriate -> SOLU SET  RFZ=2.8 TFZ=8.3 PAK=13*LLG*=-37 *LLG*=2199 as an
> example). However, I did get the following somewhat expected warnings:
>
> Number of known components (1) not divisible by 2: Translational *NCS* correction
> not applied
> Large non-origin Patterson peak indicates that translational *NCS* is
> present
> Upon any attempt at initial refinement (with a number of different
> strategies), the R-factors are hung up > 0.42 (for example in the P3121,
> 2.1Å case):
> Start R-work = 0.4966, R-free = 0.5133
> Final R-work = 0.4231, R-free = 0.4477
> *** best R-factors from ~ 15 different strategies
>
> My concern is that there is some pathology that is not being recognized
> (merohedral twinning) or that the NCS/pseudosymmetry is not being addressed
> appropriately. Any suggestions in troubleshooting this would be much
> appreciated, as I have pretty much exhausted everything I could think of.
>
> --
>   Cheers,
>     John
>
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>



-- 
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P.H. Zwart
Staff Scientist
Berkeley Center for Structural Biology, Science lead
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
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