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
