[phenixbb] bad density for part of the electron density map
wei.shi118 at gmail.com
Thu Oct 3 20:56:54 PDT 2013
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
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