| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | | |
|
|
Re: [ccp4bb] Highest shell standards |
|
CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 21 March 2007Subject: Re: Highest shell standards From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2007-03-21 > Could someone point me to some standards for data quality, especially > for publishing structures? I'm wondering in particular about highest > shell completeness, multiplicity, sigma and Rmerge. > > A co-worker pointed me to a '97 article by Kleywegt and Jones: > > _http://xray.bmc.uu.se/gerard/gmrp/gmrp.html_ > > "To decide at which shell to cut off the resolution, we nowadays tend to > use the following criteria for the highest shell: completeness > 80 %, > multiplicity > 2, more than 60 % of the reflections with I > 3 sigma(I), > and Rmerge < 40 %. In our opinion, it is better to have a good 1.8 Å > structure, than a poor 1.637 Å structure." > > Are these recommendations still valid with maximum likelihood methods? > We tend to use more data, especially in terms of the Rmerge and sigma > cuttoff. > > Thanks in advance, > > *Shane Atwell* > Hi Shane, I definately no longer support the conclusions from that 1997 paper and I think Gerard probably has adjusted his thoughts on this matter as well. Leaving out the data beyond 1.8A (in the example above) only makes sense if there is no information in those data. Completeness and multiplicity are not direct measures of data quality and the 60% I>3sigma and Rmerge <40% criteria are too strict to my liking. I prefer to look at I/SigI mostly, and as a reviewer I have no problems with highest resolution shell stats with I/SigI anywhere in the 1.5-2.5 range. I won't complain about higher I/SigI values if done for the right reasons (phasing data sets being the most common), but will say something if they state their crystals diffract to 2.5A if the I/SigI in the highest resolution shell is, let's say, 5. Their crystals don't diffract to 2.5A, they just didn't let the crystals diffract to their full potential. You can't really reject papers for that reason, but there appears to be a conservative epidemic when it comes to restricting the resolution of the data set. Bart -- ============================================================================== Bart Hazes (Assistant 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 ============================================================================== CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 21 March 2007 |
| ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd |