Partially reduced disulfides

Hi Chris,

it's a bit difficult for me to follow your description without actually looking at the structure...
Could you send me the PDB file and tell occupancies of which atoms should be refined and how, then I will try to suggest how to instruct phenix.refine to do what you want.

Pavel

On 3/22/12 7:33 PM, Christopher Wanty wrote:

Partially reduced disulfides Hi,

I have a structure that appears to have a combination of reduced and oxidised disulfides.

From previous reading on the board I’ve taken the strategy of dropping the disulfide detection cutoff to 0.1 then added back the disulfides as appropriate using restraints. The problem I now have is that for some of these cysteine pairs there are clearly oxidised and reduced positions in the density. Modelling altloc’s for each of these works, but the occupancies do not refine as I expected; the altloc’s involved in the disulfide I expected to have the same occupancy as their counterpart in the disulfide.

To try to get these to match, I introduced occupancy constraint that look like:
constrained_group {
selection = (chain A and resseq 276 and altloc B) or (chain A and resseq 286 and altloc B)
}

But with that the sum of occupancies for altloc 276 (for example) is not adding to 1.00. My thought is that I need to change the occupancy constraints but I’m not sure how to make them do what I want.

Any help/advice is appreciated.

Regards,
Chris
-------------------------------------------------------
Dr. Christopher Wanty
[email protected]

Research Associate
Biomolecular, Biomedical and Chemical Sciences,
Building M310
University of Western Australia
35 Stirling Highway
Crawley 6009
Western Australia
Australia
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