Dear list I would like some advice on how to do the final refinement of a twinned structure: I have a 3.0A structure (sg R3) which is twinned. I have collected ~50 datasets and the estimated twin-fraction varies from 0.2 to 0.45 based on phenix.xtriage analysis (britton plot etc). The structure could only be solved by experimental phasing using _detwinned_ datasets (detwinned by the ccp4 program DETWIN). Refinement of the model was initially done using my highest resolution _detwinned_ dataset (3.0A, britton_alpha:0.21) and a ML target in phenix.refine. Lately I have switched to th twin_lsq_f target and refined using the 'unmodified'/twinned dataset. 1. I have tried systematically to detwin the dataset with different twin-fractions and then refine using the ML-target and my best refinements comes using an alpha of 0.2 (see attached figure). This fits the Britton plot etc. 2. xtriage estimated the twin-fraction to by ~0.21, but using twin_lsq_f, phenix.refine now gets alpha to be 0.31. This seems like a large increase to me? 3. Using the manually detwinned dataset and a ML-target gives better R-factors than using the twin_lsq_f target (see attached figure). Bottom line: How should I report/deposit this structure: A. Should I use the manually detwinned data and an ML-target to get a model that explains the data best (lowest R-factors). And deposit my structure with modified (i.e DETWINNED) structure factors. I fear that people would react strongly to the deposition of modified F_obs in the pdb. I could deposit both twinned and detwinned structure-factores but this might also confuse? OR B. Should I use the twin_lsq_f target and accept that my deposited model is not as good as I know it could be. And deposit my structure with the real (i.e TWINNED) structure factors. OR C. Something I'm not aware of means that refinement using the ML-target is not allowed on detwinned datasets, causing me to have artificially low R-factors. I hope I'm not missing something basic here.:) Thank for any advice, pointers and ideas! -Bjørn -- Bjørn Panyella Pedersen, PhD Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco MC2240, 600 - 16th Street S414 San Francisco, CA 94158-2517 Phone: +1 415-476-3937 E-mail: [email protected] http://www.msg.ucsf.edu
