[phenixbb] problem with high Rfree

Peter Zwart PHZwart at lbl.gov
Tue May 20 01:04:50 PDT 2008

> I am working on a structure that is twinned (merohedral) in P41.  Initial
> estimates of twinning fraction (via xtriage and Yeates server) are around
> 0.37; in refinement they start around 0.49 and drop to 0.46 (so far).

One can compensate for 'model imperfection' by inflating the twin
fraction: in the early stages of refinement the twin fraction might be
seomwhat higher due to this reason.

> I should mention that data processing wasn't easy- this crystal form also
> has an apparent epitaxial twin in the b dimension causing a doubling in that
> dimension.  During indexing (with SAINT) I applied a transformation of 100
> 00.50 001 to the reflections, which then gave me the expected cell and from

What about a? Are you sure that you don't have pseudo translational
symmetry somehow?

> Xprep the data looks OK.  (Yes, I am trying to grow different forms)
> Maps look nice, although I wish my ligand had more/better density.

When twin fractions are highish, density can be rather biased. This
also means that when you don't place model atoms in a certain area,
you tend not to see density there.

> I ran phenix.refine with defaults, and included twin_law="h,-k,-l",
> xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true
> and also simulated_annealing=true.  My starting R/ Rfree is 0.448/ 0.4385;
> ending is 0.2962/ 0.4270.  Geometry is somewhat tighter after refinement but
> is better (bonds 0.017 to 0.01, angles 1.966 to 1.530).  I have not included
> my ligand, and I can see a few spots where the model needs adjusting, but
> nothing majorly wrong.

Did you try using TLS?

> Why is my Rfree hanging so high?  Is it becaues I have bad karma?

Future bad karma can be avoided by refining without attachment.

>  Is it to
> do with the twinning?  I am pretty sure my space group is right (based on
> the above info and the maps look fine; Phaser could not find a solution in
> P43).  There isn't room for anything else in the cell.

I would try TLS and recheck the unit cell parameters.


> Any opinions or suggestions are most welcome as I wait for better xtals to
> grow...
> Thanks in advance,
> Christina
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
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