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, <[log in to unmask]
> <mailto:[log in to unmask]>> 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:[log in to unmask]
> <mailto:[log in to unmask]>] *Im Auftrag von *Matthias Zebisch
> *Gesendet:* Dienstag, 10. Dezember 2013 14:21
> *An:* [log in to unmask] <mailto:[log in to unmask]>
> *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 [log in to unmask] <mailto:[log in to unmask]>____
>
> 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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