You could try the diffraction anisotropy server:
http://services.mbi.ucla.edu/anisoscale/.
Sometimes it helps maps become more interpretable.
Ben
On 26 Jan 2017, at 14:11, Pooja Kesari <[email protected]> wrote:
We have a 2.6 A structure showing four chains in an asymmetric unit. Our
protein is 360 residues around 40 kDa . Mattews shows four chain in an
assymetric unit (solvent 49% mattews coeff 2.44). The template has about 60%
homologous with our protein. The molecular replacement against this template
gave an initial free R of 38. We did chain tracing and found that we have good
density (2Fo-Fc) for chain A and B but poor density for C and D.
1. The density for a particular stretch of 10 amino acids (disordered loop
region) is absent in all the chains. We could not found density for this
flexible loop region in any of the already known structures. Any suggestion on
how can we build this region?
2. We did not find density for most of the loop regions in chain C and D which
were well traced in chain A and B. How can we improving the density for these
two chains based on chain A and B (Density modification)?
3. We analysed the data using phenix xtriage and found that our data shows
severe anisotropy. Any suggestion of anisotropy correction?
Pointless and Ctruncate analyses didn't show twinning or NCS. I have checked
the space group using Zanuda. We are stuck at a free value of 32.
On Thu, Jan 26, 2017 at 4:47 PM, Eleanor Dodson <[email protected]
<mailto:[email protected]>> wrote:
This is a bit too vague to help much.
How did you solve the structure?
Eleanor
On 26 January 2017 at 03:50, Pooja Kesari <[email protected]
<mailto:[email protected]>> wrote:
Dear All,
Thank you all for reply.
We have checked the data for twinning.
Our protein is 360 residues around 40 kDa protein.
We have tried TLS refinement.
chain A and B don't superimpose well with chain C and D. (A and B chains also
share slight difference )
Since we don't have proper density for some regions chain C and D, we are not
sure whether these chain have similar or different conformations.
We tried anisotropy correction and the model refined a bit.
On Wed, Jan 25, 2017 at 10:32 AM, Debanu <[email protected]
<mailto:[email protected]>> wrote:
Hi Pooja,
Are you positive you have the correct space group and there are no other issues
like twinning, etc?
If sure, did you define NCS groups in refinement? TLS refinement? Try different
refinement programs?
How big is the molecule? Was it solved by MR or experimental phasing?
You can try superimposing A/B on C/D and refinement with tight NCS then adjust
NCS restraints during model adjustments based on local differences or also see
if phenix autobuild helps.
Best,
Debanu
--
Debanu Das
Accelero Biostructures
On Jan 24, 2017, at 8:42 PM, Pooja Kesari <[email protected]
<mailto:[email protected]>> wrote:
> Dear All,
>
> I have a 2.6 A resolution structure having four chains in an asymmetric unit.
> The chain A and B have density for almost all residues however we don't have
> proper residue density in chain C and D.What can be tried to build chain C
> and D ?
>
>
>
> Many Thanks
> Pooja
--
Thanks & Regards,
Pooja Kesari
Research Scholar
Department Of Biotechnology
Indian Institute of Technology Roorkee
INDIA
--
Thanks & Regards,
Pooja Kesari
Research Scholar
Department Of Biotechnology
Indian Institute of Technology Roorkee
INDIA
Dr Ben Bax
Dept. Biological Chemistry,
John Innes Centre,
Norwich Research Park,
Norwich NR4 7UH, UK
[email protected]
