Dear All, Thanks so much for all of you who spent time answering my questions. These are all really great suggestions. I'll follow up with your suggestions and see how it works out with my case.
Thanks again, Eric On 7/31/07, Eric Liu <[EMAIL PROTECTED]> wrote: > > Hi All, > I would like to get some help from here for a data set I recently worked > on. I have been working on a new kinase data set which does not have a close > homolog. The data was collected to 2.1A resolution in space group P212121 > however the difference between a and b is only 0.5A. If I index the data > as P4, Rmerge is increased from 13% to 39%. I used the most close homologs > which have about 37% sequence identity as search model for molecular > replacement and it seemed I have got the solution by using Phaser with only > the c-terminal part of the search model and also a long loop removed. After > changed the different residues back to the target protein, the structure was > refined to Rfree/R 46% and 43% to 2.1 A resolution. The existing > c-terminal structure has well defined density except 25ish residue at the > very c-terminal end doesn't have well connected density. Current > model contains about 50% of overall target residues. I can see some extented > difference density for several residues going to the N-terminal part and > also extented density for the C-terminal loop for several residues. I also > see tones of not well-conncted difference density in the N-terminal region. > There was no sever clashes between molecules after mount all > symmetry related molecules. My question is the following: > > 1. Have I got the correct solution for the molecular replacement? > 2. How can I bring back the missing density for the N-terminal residues > and the loop region? > > I would really appreciate any inputs or suggestions. > > Eric >
