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

Pavel Afonine pafonine at lbl.gov
Wed Aug 4 08:07:53 PDT 2010

  Hi Joe,

Ralf correct me if there is a better way of doing this...
You can define a bond between any selected atoms:


For example:

refinement.geometry_restraints.edits {
     excessive_bond_distance_limit = 10
     bond {
       action = *add delete change
       atom_selection_1 = chain A and resseq 123 and name SG
       atom_selection_2 = chain X and resseq 345 and name S1
       symmetry_operation = None
       distance_ideal = 2.1
       sigma = 0.02
       slack = None

It is important in your case that you need to define a symmetry 
operation that relates both atoms in question. There is a trick to get 
it in Coot but I forgot (Ralf knows - he showed me at some point) - I'm 
sure it was on phenixbb a few times in the past.

After this everything should work.


On 8/4/10 4:53 AM, Joseph Noel wrote:
> Hi Ralf and Pavel,
> Unfortunately, Phenix didn't recognize a disulfide bond should exist 
> between the sulfur atoms of DTT and the side chain sulfur atom of the 
> cysteine residue in question. I position everything well in the Fo-Fc 
> and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A 
> apart. However, after refinement the DTT molecule moved so the two 
> sulfurs in question where nearly 3 A away. Maybe this is because it is 
> a mixed disulfide between a DTT molecule and a side-chain Cys rather 
> then what most programs expect which is a disulfide between two Cys 
> residues. Is it possible I need to define the complete chemical entity 
> as a hetatm (the disulfide linked Cys residue? Is there a way to 
> specify that a covalent bond should exist between the SG atom of the 
> Cys in question and the S atoms of DTT with DTT lying across the 
> crystallographic two-fold given its internal 2-fold symmetry?
> Joe

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