[phenixbb] bad density for part of the electron density map

[Wei Shi]

I am sorry I made a mistake the previous email. The density for the
N-terminal DNA binding domain is bad, not the C-terminal  DNA binding
domain. Thank you!


On Thu, Oct 3, 2013 at 11:51 PM, Wei Shi <wei.shi118 at gmail.com> wrote:

> Hi all,
> I am working with a dataset in space P212121, resolution 2.8 amstrong,
> total completeness of the data 96.2% (98.1%), I/sigma 5.2 (3.1).
> This is a structure of a transcriptional factor (dimer) with the ligand.
> Upon ligand binding, there is conformational change in some part of the
> protein and I used the apo protein structure as a search model, and get a
> molecular replacement solution. After some rounds of refinement and rebuild
> (mainly in a region in the C-terminal ligand binding domain), the best
> refinement I have is as follows. But the electron density map for the
> C-terminal DNA binding (about 80 residues) is still very bad.... I tried to
> mutate them to alanine and do refinement and also tried to delete the whole
> region to do refinement, but both of the strategies didn't give me better
> density which I could use to rebuild the residues manually. I am wondering
> whether any of you have any ideas about what might go wrong and any
> suggestions about what to check or try next. Thank you so much!
>
>                          start         final
>   ---------------------------------------
>   R-work:           0.3220        0.3100
>   R-free:           0.3916        0.3884
>   RMS(angles):      2.50          1.39
>   RMS(bonds):       0.016        0.010
>
>
>                  Ramachandran outliers:   1.8% (Goal: < 0.2%)
>                   Ramachandran favored:  89.0% (Goal: > 98%)
>                       Rotamer outliers:   5.4% (Goal: 1%)
>                        C-beta outliers:   0    (Goal: 0)
>                             Clashscore:  11.50
>                          Overall score:   2.71
>
> Best,
> Wei
>
>
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