Hi Ethan,
You are absolutely right. As a matter of fact, I had initially
processed the data to 2.7A and it looked pretty decent with R symm
less than 10%. The maps looked good too.
The problem arose during second round of refinement. The Rfree got
stuck at around 29-30 while the Rfactor kept decreasing to about
20-21. The bond length and angle values are fine too.
I cut down the resolution to 3A hoping to improve the data quality by
removing some noise. But, it did not work. i also tried to put
restrains on the backbone B factors with limited success.
Any thoughts on how i can resolve this Rfree issue?
Thanks much,
Seema
On May 20, 2011, at 5:38 PM, Ethan Merritt wrote:
> On Friday, May 20, 2011 02:28:26 pm Mittal, Seema wrote:
>> Hi All,
>>
>> I am currently working on a 3A resolution dataset. The scaled file
>> shows the following statistics (scroll down to the end of this
>> email). It is P212121 space group with R merge of 8.8%.
>
> Your data statistics look fine. In fact, it looks to me that your
> crystal is
> probably yielding good data to considerably better resolution than 3A.
> Why did you choose to cut it there?
>
>> My question is : Is there a way to selectively use only the data
>> with I/Sigma value of 2 and more for refinement?
>
> That is a bad idea. By removing data you are throwing away
> information.
> Noisy data is still better than no data.
>
> good luck with your [probably better than 3A] structure,
>
> Ethan
>
>
>> And how do i achieve this using refmac? I am aware that this would
>> come at the cost of compromising data completeness. Any
>> suggestions/help would be greatly appreciated.
>>
>>
>> Thanks much,
>> Seema Mittal
>> Department of Biochemistry & Molecular Pharmacology
>> 970L Lazare Research Building
>> University of Massachusetts Medical School
>> 364 Plantation Street
>> Worcester, MA 01605
>>
>>
>>
>>
>>
>> Shell I/Sigma in resolution shells:
>> Lower Upper % of of reflections with I / Sigma less than
>> limit limit 0 1 2 3 5
>> 10 20 >20 total
>> 50.00 6.46 2.0 3.8 5.3 6.2 7.6 12.5 34.3
>> 65.0 99.3
>> 6.46 5.13 0.7 2.2 3.9 5.3 8.2 15.7 36.6
>> 63.4 100.0
>> 5.13 4.48 1.3 2.8 4.0 5.8 9.3 13.8 27.3
>> 72.7 100.0
>> 4.48 4.07 0.7 1.7 4.0 5.4 7.9 13.9 35.4
>> 64.1 99.5
>> 4.07 3.78 1.8 3.6 5.1 6.9 11.8 20.8 49.6
>> 47.3 96.9
>> 3.78 3.56 1.5 3.8 6.7 8.7 13.3 26.7 65.4
>> 30.8 96.2
>> 3.56 3.38 0.8 3.2 7.1 8.9 12.9 31.1 76.6
>> 20.0 96.6
>> 3.38 3.23 2.0 4.8 8.1 14.8 23.4 44.8 84.7
>> 12.7 97.5
>> 3.23 3.11 4.1 9.2 13.8 18.4 29.6 51.0 86.0
>> 11.0 96.9
>> 3.11 3.00 2.4 8.6 13.9 18.8 30.6 53.9 92.4
>> 4.5 96.9
>> All hkl 1.7 4.3 7.1 9.8 15.3 28.0
>> 58.1 39.9 98.0
>>
>>
>> Shell Lower Upper Average Average Norm. Linear Square
>> limit Angstrom I error stat. Chi**2 R-fac R-fac
>> 50.00 6.46 511.7 20.0 8.8 1.098 0.065 0.073
>> 6.46 5.13 284.6 10.1 6.3 1.047 0.062 0.064
>> 5.13 4.48 500.9 17.0 8.8 1.007 0.062 0.069
>> 4.48 4.07 446.1 17.4 9.2 1.032 0.069 0.070
>> 4.07 3.78 307.1 14.5 8.4 1.065 0.089 0.092
>> 3.78 3.56 243.4 13.8 7.9 1.033 0.108 0.112
>> 3.56 3.38 182.3 12.0 8.3 1.083 0.132 0.134
>> 3.38 3.23 136.5 10.4 7.7 1.048 0.155 0.151
>> 3.23 3.11 107.4 9.2 7.3 1.096 0.184 0.163
>> 3.11 3.00 91.0 8.7 7.3 1.044 0.215 0.201
>> All reflections 287.7 13.5 8.0 1.055 0.088 0.082
>>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center, K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
>
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