Hello,
I'm observing a very strange phenomena (at least to me, I'm a beginner).
It is related to symmetry (I think).
I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas < 35% in the
last shell) and a partially refined solution with R/Rfree 22/24, 166
aminoacids observed and around 30 solvent molecules. I'll call this
Solution-1. The refinement was smooth, the densities were very clearly
"asking" for the correct missing side chains and the map looks good.
The space group I'm using is P212121, pointless and XDS agree with that
(but me and pointless both have a long history of being wrong about
space groups). Phenix.xtriage says there's no twinning.
I took Solution-1 and used it as a template in a molecular replacement
in the same space group (P212121) using the same mtz as the one used to
refine the template. I got a different (not superposed in space)
solution (called Solution-2, scores by Phaser RFZ=24.2 TFZ=33.0 PAK=0
LLG=1413 LLG=1899) that was readily refined in Phenix to R/Rfree 24/26
without any solvent molecule.
- The solutions are not superposed in space, although they are
near-identical and can be superposed yielding a C-alpha rmd =0.001.
- Both structures present VERY similar density maps. The maps are not
superposed in space, but when you "run the chain" in one map in Coot and
do the same in the other it they the present exactly the same features.
It is impossible to ignore their similarities.
- Both structures and maps present the same origin and unit cell.
- If I add to Solution-2 the equivalent solvent molecules of Solution-1
(I did this by superposing Solution-1 to Solution-2 then copy/pasting
the solvent molecules), the R/Rfree become 22/24. This is a clear
indication that the solutions are related.
- I can't find any MR solutions using the same template and space groups
P222, P2221 and P21212.
How two different sets of phases can yield maps with the same features?
What is happening, wrong space group? I have a feeling my lack of
experience is the problem.
Thank you.
Regards,
Napo
