[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!
pafonine at lbl.gov
Wed Aug 4 08:07:53 PDT 2010
Ralf correct me if there is a better way of doing this...
You can define a bond between any selected atoms:
excessive_bond_distance_limit = 10
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?
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