Sampath
With regard to your question on what sort of statistics you should get
within
structure determination you might find this service at the PDBe useful :
http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp
You can view and manipulate distributions of R, Rfree and R-Rfree along
within many other data distributions from Xray (also NMR/EM) during
structure determination. There are also links (clicking the graph) that
list
all the depositions that have a particular value within the distribution.
I agree with Pavel that from your quoted statistics that it would be
un-wise to deposit
the structure in the current state of refinement as there is clearly an
issue.
Regards
Tom Oldfield
Hi Sampath,
this is how the distribution of Rwork, Rfree and Rfree-Rwork look like
for 'all' PDB structures refined at around 2A resolution. The "<<<"
indicates where your structure stands with respect to this distribution.
Histogram of Rwork for models in PDB at resolution 1.90-2.10 A:
0.093 - 0.118 : 2
0.118 - 0.143 : 35
0.143 - 0.168 : 390
0.168 - 0.193 : 1439
0.193 - 0.218 : 1802 <<< your structure
0.218 - 0.242 : 785
0.242 - 0.267 : 159
0.267 - 0.292 : 14
0.292 - 0.317 : 1
0.317 - 0.342 : 1
Histogram of Rfree for models in PDB at resolution 1.90-2.10 A:
0.149 - 0.170 : 10
0.170 - 0.191 : 116
0.191 - 0.213 : 534
0.213 - 0.234 : 1166
0.234 - 0.255 : 1417
0.255 - 0.276 : 942
0.276 - 0.297 : 343
0.297 - 0.319 : 78
0.319 - 0.340 : 17 <<< your structure
0.340 - 0.361 : 5
Histogram of Rfree-Rwork for all model in PDB at resolution 1.90-2.10 A:
0.001 - 0.011 : 41
0.011 - 0.021 : 230
0.021 - 0.031 : 724
0.031 - 0.041 : 1210
0.041 - 0.050 : 1206
0.050 - 0.060 : 654
0.060 - 0.070 : 318
0.070 - 0.080 : 160
0.080 - 0.090 : 56
0.090 - 0.100 : 29
So, it seems your case is the example of typical overfitting, which
means the model parameterization or/and the refinement strategy is not
good for your data and model.
If you send me the data and model files then I will be able
(hopefully) to suggest a better refinement strategy or explaine why
it's not feasible with available tools. All files will be kept
confidentially.
The histograms above are obtained using this command from PHENIX family:
phenix.r_factor_statistics 2.0
Good luck!
Pavel.
On 7/7/10 10:17 PM, Sampath Natarajan wrote:
Dear all,
I have a question about the R free value. I refined a structure with
2A resolution. After model building and restraint refinement using
Refmac program, the average B factor was around 50 for all atoms. The
R/Rfree were around 22/34. Then used the TLS refinement choosing
entire molecule. Then R/Rfree reduced as 20/32. But the average B
factor was reduced as 30. The R/Rfree difference is about 12% in
final refinement. I feel it is significantly higher.
Could any one suggest me to reduce the Rfree value more? or is it
good to submit the data in the PDB database with this 12% difference?
Thanks for the suggestions.
Sincerely,
Sampath N
