I dont think there is an Rfree problem..
At 2.7A you expect quite a big difference between R and Rfree
Reducing the resolution will a) probably makethe Rfree/R difference
greater, and b) degrade the quality of your maps and model.
Eleanor
On 05/21/2011 02:28 AM, Seema Mittal wrote:
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
