[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!

[Joseph Noel]

Thanks so much Pavel for the very rapid response! One more thing, it is a disulfide linked DTT so do I do anything special to ensure that all the sulfur atoms (4 in total - two in one unit cell - one each from the cys and dtt and two in the other unit cell) stay in close enough contact for a covalent bond and not move due to non-bonded contact distance restraints?
___________________________________________________________
Joseph P. Noel, Ph.D.
Investigator, Howard Hughes Medical Institute
Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
The Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA  92037 USA

Phone: (858) 453-4100 extension 1442
Cell: (858) 349-4700
Fax: (858) 597-0855
E-mail: noel at salk.edu

Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
___________________________________________________________

On Aug 3, 2010, at 6:05 PM, Pavel Afonine wrote:

> Hi Joe,
> 
> I think all you need is summarized here:
> 
> http://www.phenix-online.org/pipermail/phenixbb/2009-December/003070.html
> 
> Please let us know if you still have any questions.
> 
> ReadySet creates a CIF file wich has nothing to do with the occupancies, symmetry etc... It just defines the geometry of your DTT. So, create a CIF file for DTT (if you really need it - I thought it is standard thing and might be already in the library) and run the refinement following the tips in the link above.
> 
> Pavel.
> 
> 
> On 8/3/10 5:54 PM, Joseph Noel wrote:
>> 
>> Hi Phenix Users,
>> 
>> I have found a beautifully ordered DTT molecule stretching across a crystallographic two-fold and linking two symmetry related cysteine side chains. Since part of this molecule sits on across the two-fold (special position) I will specify the occupancy as 0.5. I am hoping to get some information on how easy (or how difficult) it is to specify this arrangement in Phenix for refinement since it is covalent and sitting across a crystallographic two-fold (and presumably stabilizing the lattice). Will ReadySet build the appropriate CIF file if I build the DTT into the density and give it a 0.5 occupancy?
>> 
>> Joe
>> ___________________________________________________________
>> Joseph P. Noel, Ph.D.
>> Investigator, Howard Hughes Medical Institute
>> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
>> The Salk Institute for Biological Studies
>> 10010 North Torrey Pines Road
>> La Jolla, CA  92037 USA
>> 
>> Phone: (858) 453-4100 extension 1442
>> Cell: (858) 349-4700
>> Fax: (858) 597-0855
>> E-mail: noel at salk.edu
>> 
>> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
>> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
>> ___________________________________________________________
>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> 

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