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There are many many kinases with different conformations of the C terminal and N terminal domains. I would first refine the Cterminal as far as you can go - correct the sequence etc etc. Then align a selection of kinases on your C-terminal coordinates ( MSDfold at www.ebi.ac.uk/msd will return you a set ) Then look at them in the density and see if one looks better than the others.. Maybe you can try MOLREP with phase information to position the N terminal domain. Or ffear using the difference map coefficients as input. But kinases are notoriously difficult. Eleanor PS - Soetinmes Arp-Warp can do miracles - never for me, but for others.. Das, Debanu wrote: > Hi Eric, > > If your Phaser results show a high Z-score (> 8) AND high LLG AND your > solution packs without clashes AND refines (even though starting > R/Rfree is high) AND reproduces density for the model portion AND > produces some Fo-Fc density for the missing portion, most probably > your solution is correct. > Starting R/Rfree can be high, especially given that you have only ~50% > of the molecule and which may have structural differences from the > target. > > What you could try out is to manually position the second > domain/portion based on the partial density and any other information > you may have, draw a mask around this complete molecule and use this > mask for further density modification to see if you can improve the > density in the missing region. You can try several different molecular > masks with different positions of the missing portion. > > Unfortunately, if that does not help, you will have to resort to > experimental phasing. The phasing power from the partial model may not > be good enough to get complete phase information for the whole > molecule. This should be easier in your case assuming the MR solution > is right. Even if you get weak/poor derivatives, you may be able to > find heavy atoms sites using the partial MR phases and then combine > MR+experimental phases. > > Regards, > Debanu. > *From:* CCP4 bulletin board [mailto:[log in to unmask]] *On Behalf > Of *Eric Liu > *Sent:* Tuesday, July 31, 2007 2:24 PM > *To:* [log in to unmask] > *Subject:* [ccp4bb] how to bring back the missing density for half of > the structure > > 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