Hi All, Here are the summary from all the answers to my questions:
1. Try use arp/warp to build the missing part of structure. 2. Build as much as possible for the missing part and the current c-terminal domain, using as low as 0.5 contour of the 2Fo-Fc density. Generate mask and then do averaging and density modification using DM/Resolev/pirate/buccaneer. 3. Align the c-terminal part of other closest kinases to the current model, then try to find which N-terminal domain matches the difference density the best by eyeballing. 4. Look into the possiblity of twinning Thanks, 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 >
