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

Wei Shi wei.shi118 at gmail.com
Thu Oct 3 20:51:27 PDT 2013

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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