Well, galvanised iron is an old story of Zn in insuline… :-\ 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 23:58 , Katherine Sippel <katherine.sip...@gmail.com> wrote: > 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 <mbfro...@post.tau.ac.il> 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: 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 >> >> > >
