As far as sigma level is concerned, and if I remember that you are working at 3.4 angstrom resolution - this 6 sigma is VERY STRONG. I am sure it is a metal atom. But you can re-process your data preserving anomalous signal and calcule anomalous map easily done in PHENIX, less so in CCP4 and then displaying anomalous map as a difference map in COOT you MUST see strong peak on this map in the heavy atom location. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 7, 2012, at 20:13 , SD Y <ccp4...@hotmail.com> wrote: > Dear Prof. Frolow, > > During sample development I have not used anything related to Zn but could be > from traces of contamination from Tris, NaCl, DTT, EDTA, LiSO4, HEPES and > other salt which were part of auto induction media. > > I am trying to search the refence in google. Are you refering to the Book > published in 1976 titled "protein crystallography", if not could you please > kindly direct me to right reference. > > I sincerely appreciate your time and suggestion. > > Warm reagrds, > SDY > > > > > > > > > From: mbfro...@post.tau.ac.il > Subject: Re: [ccp4bb] low-resolution and zinc > Date: Wed, 7 Nov 2012 19:35:21 +0200 > To: ccp4...@hotmail.com > > Zn is always there as anything else. > If you have high affinity binding site, it will be filled with Zn (or > similar) on the various stages of your > sample development. > BTW use old Blandell&Johnson popular in my time (70-90's) approach - in the > correct space group the peak hight of this heavy atom will be the highest > comparing to other space groups > FF > Dr Felix Frolow > Professor of Structural Biology and Biotechnology, Department of Molecular > Microbiology and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica F, co-editor > > e-mail: mbfro...@post.tau.ac.il > Tel: ++972-3640-8723 > Fax: ++972-3640-9407 > Cellular: 0547 459 608 > > On Nov 7, 2012, at 19:29 , SD Y <ccp4...@hotmail.com> wrote: > > Dear all, > > I have a related question to the one I have posted "low resolution and SG", > on which I am still working based on the suggestions I have got. > > The model I have used, has Zn co-ordinated well in tetrahydral fashion by 3 > cys and 1 His residues. They have add Zn in to their experiment. > In my 3.4 A structure (I am still working on right SG), initial maps show > very strong positive density (sigma=6.5) at the place of Zn ( > https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png). I have not > used Zn in my experiment. I could only suspect Tryptone and yeast extract > which I used to make media. > > I would like to know how likely this positive density belongs to Zn? How to > reason the presence of Zn when its not been used? > Is there is any way to confirm if its Zn. If this is not Zn, what else could > it be? Any thing I could try to rule out or in Zn or other ions. > I appreciate your help and suggestions. > > Sincerely, > SDY > >
