Dear Bernhard

I am wondering where I should cut my data off. Here is the statistics 
from XDS processing.

Maia

SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONS COMPLET R-FACTOR R-FACTOR COMPARED 
I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr

10.06 5509 304 364 83.5% 3.0% 4.4% 5509 63.83 3.1% 1.0% 11% 0.652 173
7.12 11785 595 595 100.0% 3.5% 4.8% 11785 59.14 3.6% 1.4% -10% 0.696 414
5.81 15168 736 736 100.0% 5.0% 5.6% 15168 51.88 5.1% 1.8% -9% 0.692 561
5.03 17803 854 854 100.0% 5.5% 5.7% 17803 50.02 5.6% 2.2% -10% 0.738 675
4.50 20258 964 964 100.0% 5.1% 5.4% 20258 52.61 5.3% 2.1% -16% 0.710 782
4.11 22333 1054 1054 100.0% 5.6% 5.7% 22333 50.89 5.8% 2.0% -16% 0.705 878
3.80 23312 1137 1137 100.0% 7.0% 6.6% 23312 42.95 7.1% 3.0% -13% 0.770 952
3.56 25374 1207 1208 99.9% 7.6% 7.3% 25374 40.56 7.8% 3.4% -18% 0.739 1033
3.35 27033 1291 1293 99.8% 9.7% 9.2% 27033 33.73 10.0% 4.1% -12% 0.765 1107
3.18 29488 1353 1353 100.0% 11.6% 11.6% 29488 28.16 11.9% 4.4% -7% 0.750 
1176
3.03 31054 1419 1419 100.0% 15.7% 15.9% 31054 21.77 16.0% 6.9% -9% 0.741 
1243
2.90 32288 1478 1478 100.0% 21.1% 21.6% 32288 16.99 21.6% 9.2% -6% 0.745 
1296
2.79 33807 1542 1542 100.0% 28.1% 28.8% 33807 13.07 28.8% 12.9% -2% 
0.783 1361
2.69 34983 1604 1604 100.0% 37.4% 38.7% 34983 9.95 38.3% 17.2% -2% 0.743 
1422
2.60 35163 1653 1653 100.0% 48.8% 48.0% 35163 8.03 50.0% 21.9% -6% 0.754 
1475
2.52 36690 1699 1699 100.0% 54.0% 56.0% 36690 6.98 55.3% 25.9% 0% 0.745 1517
2.44 37751 1757 1757 100.0% 67.9% 70.4% 37751 5.61 69.5% 32.5% -5% 0.733 
1577
2.37 38484 1798 1799 99.9% 82.2% 84.5% 38484 4.72 84.2% 36.5% 2% 0.753 1620
2.31 39098 1842 1842 100.0% 91.4% 94.3% 39098 4.19 93.7% 43.7% -3% 0.744 
1661
2.25 38809 1873 1923 97.4% 143.4% 139.3% 38809 2.84 147.1% 69.8% -2% 
0.693 1696

total 556190 26160 26274 99.6% 11.9% 12.2% 556190 21.71 12.2% 9.7% -5% 
0.739 22619



Bernhard Rupp (Hofkristallrat a.D.) wrote:
> I think this suppression of high resolution shells via <I/sigI> cutoffs is
> partially attributable to a conceptual misunderstanding of what these (darn)
> R-values mean in refinement versus data merging. 
>
> In refinement, even a random atom structure follows the Wilson distribution,
> and therefore, even a completely wrong non-centrosymmetric structure will
> not  - given proper scaling - give an Rf of more than 59%. 
>
> There is no such limit for the basic linear merging R. However, there is a
> simple relation between <I/sigI> and R-merge (provided no other indecency
> has been done to the data). It simply is (BMC) Rm=0.8/<I/sigI>. I.e. for
> I/sigI -0.8 you get 100%, for 2 we obtain 40%, which, interpreted as Rf
> would be dreadful, but for <I/sigI> 3, we get Rm=0.27, and that looks
> acceptable for an Rf (or uninformed reviewer).  
>
> Btw, I also wish to point out that the I/sig cutoffs are not exactly the
> cutoff criterion for anomalous phasing, a more direct measure is a signal
> cutoff such as <delF/sig(delF)>; George I believe uses 1.3 for SAD.
> Interestingly, in almost all structures I played with, <delF/sig(delF)> for
> both, noise in anomalous data or no anomalous scatterer present, the
> anomalous signal was 0.8. I haven’t figured out yet or proved the statistics
> and whether this is generally true or just numerology...
>
> And, the usual biased rant - irrespective of Hamilton tests, nobody really
> needs these popular unweighted linear residuals which shall not be named,
> particularly on F. They only cause trouble.  
>
> Best regards, BR
> -----------------------------------------------------------------
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> [log in to unmask]
> [log in to unmask]
> http://www.ruppweb.org/                
> -----------------------------------------------------------------
> Structural Biology is the practice of
> crystallography without a license.
> -----------------------------------------------------------------
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Bart
> Hazes
> Sent: Thursday, March 03, 2011 7:08 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule
>
> There seems to be an epidemic of papers with I/Sigma > 3 (sometime much
> larger). In fact such cases have become so frequent that I fear some people
> start to believe that this is the proper procedure. I don't know where that
> has come from as the I/Sigma ~ 2 criterion has been established long ago and
> many consider that even a tad conservative. It simply pains me to see people
> going to the most advanced synchrotrons to boost their highest resolution
> data and then simply throw away much of it.
>
> I don't know what has caused this wave of high I/Sigma threshold use but
> here are some ideas
>
> - High I/Sigma cutoffs are normal for (S/M)AD data sets where a more strict
> focus on data quality is needed.
> Perhaps some people have started to think this is the norm.
>
> - For some dataset Rsym goes up strongly while I/SigI is still reasonable. I
> personally believe this is due to radiation damage which affects Rsym (which
> compares reflections taken after different amounts of exposure) much more
> than I/SigI which is based on individual reflections. A good test would be
> to see if processing only the first half of the dataset improves Rsym (or
> better Rrim)
>
> - Most detectors are square and if the detector is too far from the crystal
> then the highest resolution data falls beyond the edges of the detector. In
> this case one could, and should, still process data into the corners of the
> detector. Data completeness at higher resolution may suffer but each
> additional reflection still represents an extra restraint in refinement and
> a Fourier term in the map. Due to crystal symmetry the effect on
> completeness may even be less than expected.
>
> Bart
>
>
> On 11-03-03 04:29 AM, Roberto Battistutta wrote:
>   
>> Dear all,
>> I got a reviewer comment that indicate the "need to refine the structures
>>     
> at an appropriate resolution (I/sigmaI of>3.0), and re-submit the revised
> coordinate files to the PDB for validation.". In the manuscript I present
> some crystal structures determined by molecular replacement using the same
> protein in a different space group as search model. Does anyone know the
> origin or the theoretical basis of this "I/sigmaI>3.0" rule for an
> appropriate resolution?
>   
>> Thanks,
>> Bye,
>> Roberto.
>>
>>
>> Roberto Battistutta
>> Associate Professor
>> Department of Chemistry
>> University of Padua
>> via Marzolo 1, 35131 Padova - ITALY
>> tel. +39.049.8275265/67
>> fax. +39.049.8275239
>> [log in to unmask]
>> www.chimica.unipd.it/roberto.battistutta/
>> VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 
>> Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it
>>
>>     
>
>