Hello Eleanor and Roger Rowlett and everyone,
I am still having a tough time with coordinated metal refinements in
refmac ( and coot )
I followed Rogers suggestion of creating a pseudo refmac run and then
using the output cif definition for Cys -SG Zn as an input for further
refinement. Even If I did input this cif , I see that my
tetra-coordinated Zinc is pushed aside and my Cysteine SG - are
disulphide
bonded to each other creating a tetrahedral arrangement.
One caveat . The Resolution of the data is no all that spectacular
(2.5) so the whole assembly appears rather blobby with three clear Zn
spheres like I would expect in the DELFWT maps before I model in the
Zn.
The other un-related problem is that coot seems to also want to bond
Cysteines to each other when I do the real space refinement, but I
think thats because SG-Zn restraints are not part of the coot
dictionary .So the problem may very well be in the lack of a record in
the pdb output by coot that says ..dont disulfide bond these Cys. I
did check there were no explicit disulphide links defined or LINK or
LINKR.
So I am still nor refining these Cys-Zn links and have them mangled
in my pdb, so any pointers will be greatly appreciated.
Thanks for your help in advance
Hari
On Thu, May 13, 2010 at 12:50 PM, Eleanor Dodson <[log in to unmask]> wrote:
> Has anyone answered this?
> Eleanor
>
> hari jayaram wrote:
>>
>> Hi
>>
>> Am trying to build coordinated Zn+2 by CYS -SG atoms and have it
>> refine properly in refmac5.5
>>
>> I added ZN ions in Coot at the Fo-Fc peaks. Then I defined manually
>> the coordination relations in a text editor using LINK records.
>> the ions were placed in the same chain that was doing the coordination.
>>
>> LINK ZN ZN A1001 SG CYS A 487 1555 1555
>> 2.34
>>
>> I found that some of these ions refined well using refmac 5.5 and the
>> resulting pdb had LINKR records in place indicating the coordinating
>> interactions.
>>
>> For some of the Zn atoms however , the ions did refine , but coot
>> still was covalently disulphide bonding the Cys to each other rather
>> than coordinating the ZN and there were no LINKR records in the refmac
>> refined pdb file. I know these interactions are legitimate because it
>> is a known structure.Should I manually create LINKR records instead of
>> LINK records after modeling in the ions?
>>
>> What is the correct procedure to model coordinating ions and have
>> refmac treat them appropriately.
>> Thanks in advance.
>>
>> Hari
>
>
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