I think this suppression of high resolution shells via <I/sigI> cutoffs is partially attributable to a conceptual misunderstanding of what these (darn) R-values mean in refinement versus data merging.
In refinement, even a random atom structure follows the Wilson distribution, and therefore, even a completely wrong non-centrosymmetric structure will not - given proper scaling - give an Rf of more than 59%. There is no such limit for the basic linear merging R. However, there is a simple relation between <I/sigI> and R-merge (provided no other indecency has been done to the data). It simply is (BMC) Rm=0.8/<I/sigI>. I.e. for I/sigI -0.8 you get 100%, for 2 we obtain 40%, which, interpreted as Rf would be dreadful, but for <I/sigI> 3, we get Rm=0.27, and that looks acceptable for an Rf (or uninformed reviewer). Btw, I also wish to point out that the I/sig cutoffs are not exactly the cutoff criterion for anomalous phasing, a more direct measure is a signal cutoff such as <delF/sig(delF)>; George I believe uses 1.3 for SAD. Interestingly, in almost all structures I played with, <delF/sig(delF)> for both, noise in anomalous data or no anomalous scatterer present, the anomalous signal was 0.8. I havent figured out yet or proved the statistics and whether this is generally true or just numerology... And, the usual biased rant - irrespective of Hamilton tests, nobody really needs these popular unweighted linear residuals which shall not be named, particularly on F. They only cause trouble. Best regards, BR ----------------------------------------------------------------- Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ ----------------------------------------------------------------- Structural Biology is the practice of crystallography without a license. ----------------------------------------------------------------- -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bart Hazes Sent: Thursday, March 03, 2011 7:08 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule There seems to be an epidemic of papers with I/Sigma > 3 (sometime much larger). In fact such cases have become so frequent that I fear some people start to believe that this is the proper procedure. I don't know where that has come from as the I/Sigma ~ 2 criterion has been established long ago and many consider that even a tad conservative. It simply pains me to see people going to the most advanced synchrotrons to boost their highest resolution data and then simply throw away much of it. I don't know what has caused this wave of high I/Sigma threshold use but here are some ideas - High I/Sigma cutoffs are normal for (S/M)AD data sets where a more strict focus on data quality is needed. Perhaps some people have started to think this is the norm. - For some dataset Rsym goes up strongly while I/SigI is still reasonable. I personally believe this is due to radiation damage which affects Rsym (which compares reflections taken after different amounts of exposure) much more than I/SigI which is based on individual reflections. A good test would be to see if processing only the first half of the dataset improves Rsym (or better Rrim) - Most detectors are square and if the detector is too far from the crystal then the highest resolution data falls beyond the edges of the detector. In this case one could, and should, still process data into the corners of the detector. Data completeness at higher resolution may suffer but each additional reflection still represents an extra restraint in refinement and a Fourier term in the map. Due to crystal symmetry the effect on completeness may even be less than expected. Bart On 11-03-03 04:29 AM, Roberto Battistutta wrote: > Dear all, > I got a reviewer comment that indicate the "need to refine the structures at an appropriate resolution (I/sigmaI of>3.0), and re-submit the revised coordinate files to the PDB for validation.". In the manuscript I present some crystal structures determined by molecular replacement using the same protein in a different space group as search model. Does anyone know the origin or the theoretical basis of this "I/sigmaI>3.0" rule for an appropriate resolution? > Thanks, > Bye, > Roberto. > > > Roberto Battistutta > Associate Professor > Department of Chemistry > University of Padua > via Marzolo 1, 35131 Padova - ITALY > tel. +39.049.8275265/67 > fax. +39.049.8275239 > roberto.battistu...@unipd.it > www.chimica.unipd.it/roberto.battistutta/ > VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 > Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it > -- ============================================================================ Bart Hazes (Associate Professor) Dept. of Medical Microbiology& Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================
