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 <[log in to unmask]> 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: [log in to unmask]
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Steiner, Roberto [[log in to unmask]]
> Sent: Friday, June 14, 2013 12:58 PM
> To: [log in to unmask]
> 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. [log in to unmask]
>
> 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 <[log in to unmask]>
> 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
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>> *******************************************************
>>
>
> Roberto A. Steiner
> Group Leader
> Randall Division of Cell and Molecular Biophysics
> King's College London
> [log in to unmask]
>
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