It doesn't look like you left a CN on your gold atom. These things
are pretty much covalently bound.

Dale Tronrud

On 12/10/2013 08:13 AM, PriyankMaindola wrote:
> dear all:
> I. i am not able to fit trp, 
> since 
> 1. trp doesnt fit well
> 2. positive density comes in fo-fc map after refinement
> 3. this is a soaked crystal str with heavy atom soln, the native one has
> perfect density for gln, so mutation to trp is unlikely
> 
> II. on increasing contour level, 2fo-fc map fades above 4.5 rmsd if I do
> not put anything in the blob and see the refined map
> 
> III. placing Au+ and refining (occ 1 ; B-fac 63 A2) gives figure 4.png
> (attached below)
> however anomalous diff map does give positive density but not a clear
> round, spherical one.
> 
> 
> On 10 December 2013 19:29, <herman.schreu...@sanofi.com
> <mailto:herman.schreu...@sanofi.com>> wrote:
> 
>     My first guess was also a metal ion. However, a tryptophan as Fred
>     suggested cannot be ruled out. A simple preliminary test is to
>     scroll up the contouring level and look when the contours of the
>     blob disappear. If the contours quickly disappear, you have
>     something disordered or light. If the contours of the blob disappear
>     at the same moment or later as e.g. sulfur atoms, you have something
>     heavy like a metal ion. You still have to fit all possibilities and
>     see what refines best.____
> 
>     __ __
> 
>     Best,____
> 
>     Herman ____
> 
>     __ __
> 
>     *Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
>     <mailto:CCP4BB@JISCMAIL.AC.UK>] *Im Auftrag von *Matthias Zebisch
>     *Gesendet:* Dienstag, 10. Dezember 2013 14:21
>     *An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>     *Betreff:* Re: [ccp4bb] Fwd: undefined edensity blob at glutamine
>     sidechain____
> 
>     __ __
> 
>     check an anomalous map!
>     The obvious thing to do to rule out gold binding
> 
>     ____
> 
>     -----------------------------------------____
> 
>     Dr. Matthias Zebisch____
> 
>     Division of Structural Biology,____
> 
>     Wellcome Trust Centre for Human Genetics,____
> 
>     University of Oxford,____
> 
>     Roosevelt Drive,____
> 
>     Oxford OX3 7BN, UK____
> 
>     __ __
> 
>     Phone (+44) 1865 287549; ____
> 
>     Fax (+44) 1865 287547____
> 
>     Email matth...@strubi.ox.ac.uk <mailto:matth...@strubi.ox.ac.uk>____
> 
>     Website http://www.strubi.ox.ac.uk____
> 
>     -----------------------------------------____
> 
>     On 12/10/2013 12:44 PM, PriyankMaindola wrote:____
> 
>         ​____
> 
>         dear members____
> 
>         __ __
> 
>         i am trying to solve this crystal structure but  ____
> 
>         ​I am puzzled with an​____
> 
>          undefined  blob ____
> 
>         ​that​____
> 
>           ____
> 
>         ​appeared at a glutamine residue after refinement. I have
>         attached pics of that below. ____
> 
>         Is it a covalent modification of acid-amide side chain.. ____
> 
>         ​... as there is no charged environment around and density seems
>         continuous.____
> 
>         __ __
> 
>         ​please suggest____
> 
>         ​____
> 
>         ....____
> 
>         __ __
> 
>         following reagents were encountered by protein ____
> 
>         ​during purification, crystallization and soaking​____
> 
>         :____
> 
>         phenyl methyl sulfonyl fluoride____
> 
>         benzamidine____
> 
>         tris____
> 
>         dtt ____
> 
>         ​ (could it be cyclized dtt?)​____
> 
>         __ __
> 
>         k[au(cn)2]____
> 
>         acidic pH____
> 
>         isopropanol____
> 
>         citrate____
> 
>         sulfate____
> 
>         phosfate____
> 
>         K+, Na+, Cl-____
> 
> 
>         ____
> 
>         ​map contour:
>         2fo-fc: 1rmsd____
> 
>         fo-fc (green): 3 rmsd​____
> 
>         __ __
> 
>         __ __
> 
>         -- ____
> 
>         *Priyank*____
> 
>     __ __
> 
> 
> 
> 
> -- 
> *Priyank Maindola*

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