As a follow up to Roger's statement if you are doing any sort of analytical metal analysis be careful with the controls (metal-free water/acid washed glassware). Also most AC/heating systems include galvanized steel in the duct work that spits out Zn like crazy and can screw up your measurements. If you have access to a neurotically OCD analytical chemist to assist I'd suggest plying them with coffee and complements.
Cheers, Katherine On Wed, Nov 7, 2012 at 3:41 PM, Felix Frolow <[email protected]>wrote: > 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: [email protected] > Tel: ++972-3640-8723 > Fax: ++972-3640-9407 > Cellular: 0547 459 608 > > On Nov 7, 2012, at 20:13 , SD Y <[email protected]> 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: [email protected] > Subject: Re: [ccp4bb] low-resolution and zinc > Date: Wed, 7 Nov 2012 19:35:21 +0200 > To: [email protected] > > 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: [email protected] > Tel: ++972-3640-8723 > Fax: ++972-3640-9407 > Cellular: 0547 459 608 > > On Nov 7, 2012, at 19:29 , SD Y <[email protected]> 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 > > > > >
