Hi Boaz, The improvement you see in the cofactor geometry after inclusion of higher resolution data is very interesting, but is it possible that this is a "secondary" effect resulting from the additional Xray data changing the relative weighting of the Xray and stereochemical terms in the refinement ?
Could you get a similar geometry improvement simply by changing the relative weighting (using only the original data) or would this only be with a penalty in other statistics ? Did you quantify the improvement in the cofactor density, for example by a correlation coefficient ? Cheers, Andrew On 14 Jun 2013, at 13:45, Boaz Shaanan <bshaa...@exchange.bgu.ac.il> wrote: > In their paper K & D monitored the electron density for their coffactor and > could verify that adding higher resolution shells based on the CC1/2 > statistics improved the way it looked. I'm not sure they monitored > bond-distances and/or esd's but those may well have been affected by > restraints and weights anyway, in the reoslution they worked (~1.45 A?). It > might be more difficult to judge the effect of including higher resolution > shells if there isn't a feature that is easy to monitor as you increase the > resolution. In one of the cases that I'm working on I certainly noticed > better geometry and e.d. for the co-factor upon adding (somewhat) higher > resolution shells. > > Cheers, > > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Steiner, > Roberto [roberto.stei...@kcl.ac.uk] > Sent: Friday, June 14, 2013 12:58 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Concerns about statistics > > BTW there's a also an earlier paper (properly cited in Karplus & Diederichs > 2012) showing the benefit of weak 'high-resolution' reflections. > > Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000. doi: > 10.1107/S0907444910029938. Epub 2010 Aug 13. > Inclusion of weak high-resolution X-ray data for improvement of a group II > intron structure. > Wang J. > Department of Molecular Biophysics and Biochemistry, Yale University, New > Haven, CT 06520, USA. jimin.w...@yale.edu > > Abstract > It is common to report the resolution of a macromolecular structure with the > highest resolution shell having an averaged I/sigma(I) > or = 2. Data beyond > the resolution thus defined are weak and often poorly measured. The exclusion > of these weak data may improve the apparent statistics and also leads to > claims of lower resolutions that give some leniency in the acceptable quality > of refined models. However, the inclusion of these data can provide > additional strong constraints on atomic models during structure refinement > and thus help to correct errors in the original models, as has recently been > demonstrated for a protein structure. Here, an improved group II intron > structure is reported arising from the inclusion of these data, which helped > to define more accurate solvent models for density modification during > experimental phasing steps. With the improved resolution and accuracy of the > experimental phases, extensive revisions were made to the original models > such that the correct tertiary interactions of the group II intron that are > essential for understanding the chemistry of this ribozyme could be described. > > Best wishes > Roberto > > On 14 Jun 2013, at 10:43, Dirk Kostrewa <kostr...@genzentrum.lmu.de> > wrote: > >> Dear Andrea, >> >> I agree with Tim and still cut the resolution at <I/sigma>=2. In my >> experience, including higher resolution shells with poorer signal-to-noise >> never changed the apparent resolution of the electron density maps. >> In addition, the high resolution limit at <I/sigma>=2 coincides very well >> with the point where the Fo vs. Fo +Gauss(0,1)*sigma(Fo) correlation >> coefficient curve, reported by BUSTER, crosses the recommended lower limit >> of 0.9. >> >> And please note, CC*=0.5 corresponds to CC(1/2)=0.143. In my very limited >> experience, <I/sigma>=2 corresponds to roughly CC(1/2)~0.7. >> >> Although I'm very excited about the CC(1/2) or CC* paper by Karplus & >> Diederichs, I still prefer to be on the save side, until it has been >> verified in numerous cases, that choosing high resolution cutoffs based on >> CC(1/2) really leads to higher resolution structures. The recommended >> procedure to include small resolution increments in refinement to decide the >> high resolution cutoff is very time-consuming. >> >> Best regards, >> >> Dirk. >> >> >> Am 13.06.13 17:15, schrieb Andrea Edwards: >>> Hello group, >>> I have some rather (embarrassingly) basic questions to ask. Mainly.. when >>> deciding the resolution limit, which statistics are the most important? I >>> have always been taught that the highest resolution bin should be chosen >>> with I/sig no less than 2.0, Rmerg no less than 40%, and %Completeness >>> should be as high as possible. However, I am currently encountered with a >>> set of statistics that are clearly outside this criteria. Is it acceptable >>> cut off resolution using I/sig as low as 1.5 as long as the completeness is >>> greater than 75%? Another way to put this.. if % completeness is the new >>> criteria for choosing your resolution limit (instead of Rmerg or I/sig), >>> then what %completeness is too low to be considered? Also, I am aware that >>> Rmerg increases with redundancy, is it acceptable to report Rmerg (or Rsym) >>> at 66% and 98% with redundancy at 3.8 and 2.4 for the highest resolution >>> bin of these crystals? I appreciate any comments. >>> -A >> >> -- >> >> ******************************************************* >> Dirk Kostrewa >> Gene Center Munich >> Department of Biochemistry >> Ludwig-Maximilians-Universität München >> Feodor-Lynen-Str. 25 >> D-81377 Munich >> Germany >> Phone: +49-89-2180-76845 >> Fax: +49-89-2180-76999 >> E-mail: kostr...@genzentrum.lmu.de >> WWW: www.genzentrum.lmu.de >> ******************************************************* >> > > Roberto A. Steiner > Group Leader > Randall Division of Cell and Molecular Biophysics > King's College London > roberto.stei...@kcl.ac.uk > > Room 3.10A > New Hunt's House > Guy's Campus > SE1 1UL > London > > Phone 0044 20 78488216 > Fax 0044 20 78486435
