But that wouldn’t incorporate other useful information, such as percentage completeness in the outer shell and whether inclusion of the reflections in the outer shell for refinement actually effects the resulting structural model and map to a significant degree.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 [email protected]<mailto:[email protected]> (214) 645-6383 (phone) (214) 645-6353 (fax) On Feb 28, 2020, at 10:03 AM, Phoebe A. Rice <[email protected]<mailto:[email protected]>> wrote: EXTERNAL MAIL Can we get some momentum for the "standard table 1" including TWO numbers - outer limit used in refinement, and nominal resolution based on some standard such as I/sigI =2 (or 3, or whatever the community can agree on)? That would hopefully cut down on all the reviewer complaints of overstated resolution. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" <[email protected]<mailto:[email protected]> on behalf of [email protected]<mailto:[email protected]>> wrote: Dear colleagues, I agree with all the previous responses, it is a pity to throw away useful high-resolution data. The problem of high-resolution cutoff estimation is also nicely summarized in another paper by Andrew Karplus and Kay Diederichs "Assessing and maximizing data quality in macromolecular crystallography" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ . It is suggested using CC1/2 for the selection of the cutoff for data processing (not I/sigI or R_whatever). Later on, the decision should be validated performing the paired refinement protocol. Good luck with the argumentation. Martin On 2/28/20 11:08 AM, LMB wrote: Ask the referee - (apart from the other suggestions here) ‘How would removing data Improve my model?” Sent from my iPad On 28 Feb 2020, at 08:22, dusan turk <[email protected]<mailto:[email protected]>> wrote: Hi, Browsing through the recent discussion on EM data resolution cutoff it occurred to me that the X-ray diffraction community isn’t that unanimous either. My stand: When the default resolution cutoff provided with the data processing software in electron density map calculation and refinement delivers quality maps noisier than expected and/or too high R-factors I start adjusting the resolution cutoff by lowering the resolution and trying alternative space group. Hence, I allow the data processing programs to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R sym, R p.i.m. and R r.i.m, …) , unless there are problems. Doing so, I came into a dispute with a referee who shaped his request: "It is well accepted that the criteria for resolution cutoff should consider both I/SigI and Rmerge for the outer most shell. For data sets collected at synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as a good practical reference.” So where do we stand? Which are the most objective criteria for resolution cutoff to be used in diffraction data processing? Which number of shells to use when calculating the statistics? Do we have a consensus? best wishes, dusan turk Dr. Dusan Turk, Prof. Head of Structural Biology Group http://stef.ijs.si/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ e-mail: [email protected] phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. 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