With significant translational pseudosymmetry, at least close to a pseudo-centerering vector, will inevitably lead to higher R-values. Basically the R-value isn’t a very good indicator of the structure correctness any more and the expected values for an acentric structure are no longer really valid. I had a somewhat similar case long ago (https://doi.org/10.1107/S0907444906031519) and since then there is a nice paper summarising the effects of pseudosymmetry (https://doi.org/10.1107/S090744490705531X).

_____________________

Esko Oksanen, PhD

Instrument Scientist - Neutron Macromolecular Crystallography

European Spallation Source ERIC

P.O Box 176, SE-221 00 Lund, Sweden

Visiting address: Odarslövsvägen 113 224 84 Lund Sweden

Switchboard: +46 46 888 00 00

Phone: +46 721 79 20 36

E-mail: [email protected]

www.ess.eu

On 27 Jan 2021, at 11:46, Jorge Iulek <[email protected]> wrote:

Dear all,

    I have a dataset at 2.98 A resolution, images processed to CC_1/2 at circa 50% in the last resolution shell, tetramer in the asymmetric unit, local (rotational) symmetry 222. Xtriage indicates a peak in the Patterson function at 20% height of origin peak, at fractional coordinates of 0.0000 0.0000 0.3177. Space group is P21.

     I am aware that this brings problems to refinement , as even stated at xtriage output "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 refinement.", and so I can't lower my R and R-free below ~31 and 36 % , respectively.

    At phenix.refine, setting "tncs_correction = True" brings little benefit (what does this actually do? points to references are welcome). I wonder nevertheless if some strategy might help in on lowering these R's and, of course, allow me to build a better model (in spite of the resolution). I tried some combinations of other types of ncs and tls groups, with little success. Particularly, it seems that the refinement of ADPs are a kind of unstable (what I would understand come from the - partial - modular nature of the intensities - due to tncs - and these - ADP - would be reflected by the intensity fall-off with resolution). What about refining ADPs only to a zone which is not affect by data modulation? How to do that? Any other ideas?

    Thanks,

Jorge

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