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

John Bruning jmbruning at gmail.com
Fri Jul 10 14:41:25 PDT 2015

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
​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*
not applied
Large non-origin Patterson peak indicates that translational *NCS* is
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.

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