Hi Mohamed,
Did you try CSO or CSD?
I've seen oxidation of Cys residues in the active site of Cysteine-dependent
Phosphatases before.
In addition, oxidation is more easily explainable than CSS and SMC, especially
if reducing agents were omitted from final purification steps.
HTH,
Dave
--
Dr David C Briggs
Hohenester Lab
Department of Life Sciences
Imperial College London
UK
http://about.me/david_briggs
From: Mohamed Noor
Sent: Sunday, 21 May, 13:00
Subject: [ccp4bb] Cys modification - deciding between CSS and SMC
To: ccp4bb@jiscmail.ac.uk
I am working on a model at a resolution of 2.1 A. The active site Cys in both
copies have a positive density towards the S end of the residue and these blobs
are there in FEM and Polder maps. When I replace these residues with either CSS
or SMC, I get the following statistics. What is the best way of deciding which
one is correct? CSS: R/Rfree - 0.2016/0.2299 Local CC (chain A/B) - 0.950/0.937
Bfactor (chain A N/CA/C/O/CB/SG/SD) - 42.8/48.6/46.7/42.8/57.3/66.2/98.8
Bfactor (chain B N/CA/C/O/CB/SG/SD) -42.0/44.5/47.2/45.7/57/60.3/95.3 No
residual positive density left. SMC: R/Rfree - 0.2087/0.2299 Local CC (chain
A/B) - 0.903/0.886 Bfactor (chain A N/CA/C/O/CB/SG/CS) -
43.9/47.9/46.5/42.1/51.8/64.4/66.5 Bfactor (chain A N/CA/C/O/CB/SG/CS) -
43.4/45.0/47.3/45.4/51.8/59.4/66.1 Crescent shaped positive density left
towards the CS atom end. Although CSS seems more plausible, the high B factors
of SD make me wonder if they are correct. Thanks. Mohamed
