[phenixbb] modelling of a novel protein

intekhab alam faisaldbg at gmail.com
Tue Dec 7 06:10:20 PST 2010

I am trying to solve the structure of RNA polymerase in complex with its
protein primer. The size of protein primer is 70 amino acids which i
complexed with the polymerase and collected a data of the complex crysta at
2.3A. The space group is C2  and after Molecular replacemnet with full
length polymerase in auto MR i got 3 subunits in ASU.
The parameters of MR solution  RFZ=71.5 TFZ=41.2 PAK=0 LLG=8812 suggests
that the solution is correct. I used autobuild for model building which gave
me the model of the polymerase as well as some extra density that i am
considering as the other protein. After several round of refinemnt i have R
and R free of 27and 32 respectively.

My queries:
 1. I want to know ,how can i improve my R as well as R free.
 2. How can i model  other protein as the density is weak and not complete,
how can i improve the map of the other protein so that i can b ebale to
trace the c-alpha backbone, i was able to model only 10 amino acids so far.

Please guide.


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