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