Hi Graeme, I agree with everything that Pavel pointed out yesterday. I have added below a tabulation of R/Rfree for a set of 46 structures from the PHENIX library, solved with autosol and then built with autobuild. You will see that your result is not unprecedented (e.g., the p9 structure), but a slightly larger spread of 0.02 to 0.06 is more common: R Rfree Resolution structure 0.17 0.24 1.80 pen 0.17 0.22 2.80 rh-dehalogenase 0.18 0.23 2.52 flr 0.19 0.25 2.40 mev-kinase 0.20 0.21 1.75 p9 0.20 0.24 2.25 gpatase 0.20 0.23 2.50 aep 0.20 0.23 1.90 myoglobin 0.21 0.24 2.80 s-hydrolase 0.21 0.23 2.40 cyanase 0.21 0.26 2.00 tryparedoxin 0.22 0.25 1.80 mbp 0.22 0.26 2.00 cobd-sad 0.22 0.25 1.95 nsf-n 0.22 0.27 2.50 psd-95 0.22 0.25 3.00 1038B 0.22 0.30 2.60 gene-5 0.22 0.25 1.80 epsin 0.23 0.28 2.50 p32 0.23 0.26 2.40 armadillo 0.23 0.27 2.40 nsf-d2 0.23 0.26 1.80 ic-lyase 0.24 0.30 2.80 cp-synthase 0.24 0.29 2.30 vmp 0.24 0.26 1.10 calmodulin 0.24 0.36 3.00 hn-rnp 0.25 0.28 2.00 synapsin 0.26 0.27 1.70 insulin 0.26 0.28 2.80 ut-synthase 0.26 0.29 1.71 1063B 0.26 0.31 2.50 rnase-s 0.26 0.30 2.33 gran-orig 0.28 0.30 1.50 rnase-p 0.28 0.34 3.00 1071B 0.29 0.34 2.50 1102B 0.29 0.36 2.60 rab3a 0.29 0.33 2.00 1167B 0.30 0.35 2.70 gere 0.30 0.33 2.10 pdz 0.30 0.32 1.90 rop 0.34 0.40 3.30 sec17 0.35 0.43 2.50 qaprtase 0.41 0.47 3.20 synaptotagmin 0.41 0.48 3.80 groel 0.43 0.48 2.90 fusion-complex 0.43 0.47 3.50 group2-intron All the best, Tom T
Hi Folks,
Quick question about R/Rfree from phenix - I ran the autobuild and it kindly built pretty much all of the visible residues, and it gave me the following output:
SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.22 0.23 169 169 2 2 0.21 0.23 170 170 3 4 0.22 0.23 170 170
Now, I'm not one to complain about good results, but I did feel that the Rfree looked a little close to the R factor - usually I would expect a difference of maybe 4-5%. Is there a reason for this that I am missing? The model seemed to fit very nicely, closely corresponded to the PDB entry and the waters were pretty good. There is no NCS (one copy in the ASU) and the phases are from SeMet mad data from Autosol.
Resolution is ~1.6A, if that is any help.
Just noticed this and thought it was interesting. I am used to Arp/wArp for automated tracing, which typically gives a bigger difference...
Many thanks,
Graeme _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb