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*
