Dear all,
Thank you for all your suggestions. I made a mistake yesterday, the space group should be C2, sorry. I did try the search model with poly-ala but got similar result. Unfortunately, there is no NCS. I had only got one crystal so I cannot do multi-averaging or seeding. HHpred gave me a few more hits which might have a similar fold to part of the first domain, I am now trying that with my partial solution but haven't got anything better yet. Things like Buccaneer and breaking the search model into domains have also been tried.
Tristan,
iMDFF building sounds really interesting, unfortunately, I am far away from the minimum requirement. My best PC is on Windows and I have only got two 5-year old ubuntu machines. Sorry.
Ronan,
I used the server to run MrBump. That would be very nice if you could have a look at my MrBump log file.
Anyway, I have got a lot of ideas from you all, I will keep trying what you suggested with my two difficult cases and let you know if there is anything good. Thanks again.
All the best,
Jason
University College London
On 26/05/16 13:29, Jason wrote:
> Dear ccp4 users,
>
> I have been trying to solve the structure of a protein which has 760
> residues. The protein has three domains and there is no homologue
> structure for the first domain which is about 300 residues. The top
> hit from PDB blast gave an identity of 36%. The resolution was 2.97 A.
> I have tried different Molecular Replacement programs with different
> models, the best solution, which was a partial solution, was from
> MrBump and had only the last two domains in the structure. These two
> domains fit in the density well and I have manually built that part a
> few time, so I am afraid that there is nothing I could do with these
> two domains at this stage. The Rfactor and Rfree are about 31% and 37%
> now. I have also tried many tracing and autobuild programs from both
> ccp4 and phenix, nothing really helped. Things like phase improvement
> and solvent flattening have also been tried. I could definitely see
> some density map for the first domain but it is difficult to trace the
> chain from coot at this resolution. The statistics are all ok with a
> P21 space group. I did check other possibilities of the space group.
> This crystal was from a screening and I could not reproduce it at this
> stage.
> So does anyone have any experience in solving this kind of problem?
> Actually, I also have another similar case at the moment.
> Many thanks in advance.
>
> All the best,
>
> Jason
>
> University College London
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