Hi Sadaf, Most likely you are dealing with radiation damage. If that's the case, you would need to refine occupancies as Mario has already suggested. However, you may not find a double conformation. Instead, you may find that some of your sulfurs are "gone". There is a ton of publications on this topic, take a loo.
If you have high enough redundancy, you may be able to use only the part of the data, collected at the beginning. This would have suffered less from radiation. You can also use "zero dose extrapolations" - look up Diederichs' and Borek's publications. Good luck! Nukri -----Original Message----- From: CCP4 bulletin board on behalf of sadaf iqbal Sent: Sun 3/6/2011 12:57 PM To: [email protected] Subject: [ccp4bb] disulfide bridge in red density Hello everyone, Recently, i have solved a protein structure at 1.3 Å resolution. I have encountered one problem in this structure while refining in COOT. There are three disulfide bridges in my structure and if i used 2.0 Å resolution range in refmac then the density around disulfide bridges is ok but if i used 1.3 Å resolution range in refmac then red density is appeared along with blue one. Can anybody help me in this regard? I already played by increasing temperature factor of sulfur atoms but red density is still there. Thanks in advance Sadaf Iqbal PhD Scholar ICCBS, University of Karachi, Pakistan. & Visiting Scientist University of Hamburg, Germany.
