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

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