Oops I meant your I/sd is 8.8 in the highest resolution bin. F On Apr 3, 2012, at 11:05 AM, Nathaniel Echols wrote:

On Tue, Apr 3, 2012 at 9:59 AM, Christian Roth wrote:

...

After refinement I have a R/Rfree of 0.1294/0.1670. In some shells there are values close to 0.100 and in the lowest shell Rfree is lower than Rwork.

Are you absolutely certain that you used the same R-free flags throughout refinement?

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Is there an equivalent of phenix.r_factor_statistics for other parameters like RMSD bond angles/lengths? I note you can get histograms in the GUI version of polygon but only when you input a pdb file for validation. Thanks, Simon On 3 Apr 2012, at 18:41, Pavel Afonine wrote:

Hi Christian,

this is kind of Rwork/Rfree that you would get if you take a very high resolution structure, may be 1.2-1A and higher, cut the data off at 2.2A, and refine it again. So one explanation is that your crystals could probably diffract to a higher resolution...

The command

phenix.r_factor_statistics 2.2

gives typical R-factors at around 2.2A resolution are:

Histogram of Rwork for models in PDB at resolution 2.10-2.30 A: 0.115 - 0.137 : 9 <<< you are here 0.137 - 0.159 : 121 0.159 - 0.182 : 703 0.182 - 0.204 : 1637 0.204 - 0.226 : 1749 0.226 - 0.248 : 735 0.248 - 0.270 : 147 0.270 - 0.293 : 12 0.293 - 0.315 : 2 0.315 - 0.337 : 2 Histogram of Rfree for models in PDB at resolution 2.10-2.30 A: 0.157 - 0.181 : 20 <<< you are here 0.181 - 0.205 : 163 0.205 - 0.229 : 784 0.229 - 0.253 : 1733 0.253 - 0.277 : 1617 0.277 - 0.301 : 671 0.301 - 0.325 : 101 0.325 - 0.349 : 22 0.349 - 0.373 : 5 0.373 - 0.397 : 1 Histogram of Rfree-Rwork for all model in PDB at resolution 2.10-2.30 A: 0.001 - 0.011 : 47 0.011 - 0.021 : 176 0.021 - 0.031 : 533 0.031 - 0.041 : 997 <<< you are here 0.041 - 0.050 : 1306 0.050 - 0.060 : 1062 0.060 - 0.070 : 602 0.070 - 0.080 : 216 0.080 - 0.090 : 113 0.090 - 0.100 : 65 Number of structures considered: 5117

Pavel

On 4/3/12 9:59 AM, Christian Roth wrote:

...

Dear Phenix people,

is there a major improvement in the algorithm? I have refined a 2.2 Ang. room temperature dataset with very good data statistics (I think) Rmerge 3.7%(8.9%) completeness 96%(92%) I/sigI 16,6(8,8) in parentheses are the values for the highest resolution shell.

After refinement I have a R/Rfree of 0.1294/0.1670. In some shells there are values close to 0.100 and in the lowest shell Rfree is lower than Rwork. The quality of the data are really quite good, what is probably one of the reasons, but I am close or below to the border of the Range of R values in the pdb. Great for me, but I wanna be sure that it is really true. It was a MolRep with a close homolog, but I run a torsion angle sim annealing to decouple R/Rfree and the MolRep was done with an poly-Ala model to prevent too much model bias.

Best Regards

Christian

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