[phenixbb] Update: Check for radiation-induced reduction of a disulfide bond - PS

Engin Özkan eozkan at uchicago.edu
Mon Feb 15 05:32:56 PST 2016

I agree with Pavel. Disulfides are hit by radiation damage, and I 
usually observe "partially reduced" disulfides in datasets I collect at 
synchrotrons. If that is the case, the solution is to create alternate 
conformations for the cysteines involved. Make sure the reduced 
cysteines have the same altloc, and are moved into positive mFoFc 
density, so that Phenix does not automatically link them as disulfides.


On 2/15/16 2:46 AM, Pavel Afonine wrote:
> P.S.:
> If atom is misplaced normally you would see both: positive and 
> negative residual density in close proximity to each other.
> If you only see negative density at SG centers this may mean the site 
> is partially occupied.
> Pavel
>> Sorry, my previous email was incomplete. My structure has negative 
>> density in the center of some disulfides (the magnitude of this 
>> effect vary between different monomers in the ASU). I'd like to 
>> refine the structure in an "artificial reduced form", where cysteines 
>> involved in disulfides are treated in reduced form, but repulsions 
>> originating from neighboring sulfur atoms are turned-off, to monitor 
>> distances (I expect that SG atoms remain close to 2 A), guided only 
>> by data. Thank you,
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