[phenixbb] Rfree refuse to come down

#HEW KAI LI KELLY# KLHEW1 at e.ntu.edu.sg
Thu Mar 1 19:34:19 PST 2012


I have a few questions about a dataset that I am working on currently.

So I ran Xtraige and it tells me that other than pseudoNCS, there is no other problems like twinning etc. And then I used autoMR and Phaser from Phenix to run molecular replacement with a the structure of the same protein (but that is with DNA bound). The TFZ is more than 9 after from both the runs. Autobuild managed to build the 4 molecules in my ASU (Rfactor/Rfree = 28/32 for a resolution of 2.4A). But because there are some clashes and outliers in the Ramachandran Plot etc, I started to manually refine them in coot. In addition, there is a loop that is unable to fit into the density, so I chopped about 10 residues off each molecule in the ASU.

However, as I started to refine the model from AutoBuild, my Rfree begins to climb. So currently, I am at Rfactor/Rfree=27/36. I don't know if there is anything wrong with I had done. So many thanks in advance for your advices on this!!

Warmest Regards,
Kelly Hew

Nanyang Technogical University
School of Biological Sciences
Division of Structural Biology & Biochemistry
Address : #07-01, IMCB, 61 Biopolis Drive, Proteos, Singapore 138673
Telephone (O): +65 65869673
Telephone (HP): +65 98713553

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