I do not see with what you do not agree in what was written (maybe not very carefully). One determine space group looking on systematic absences, this I know. Space groups P41 - P43 ( I do not go to more general discussion for the sake of argument) are not distinguishable and one have to try molecular replacement in both. Most probably the correct space group will give a sensible solution and wrong one will not. I was talking about distinguishing between point groups P4 and P422. I hope you grew that they CAN be distinguished on the level prior to molecular replacement? And I hope that you agree that starting refinement of demanding project at relatively low resolution such as 3.4 Angstrom it is advisable to characterise space group, twinning status etc.? If you agree also to that, with what you do not agree? 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 8, 2012, at 12:20 , herman.schreu...@sanofi.com wrote: > Dear Dr. Frolow, > > I do not agree. In the absence of heavy atom/anomalous data, the only way to > distinguish e.g. between P41 and P43 is with molecular replacement. On could > do it automatically, like is implemented in modern programs, or run MR in > different space groups manually, but one has to test the various > possibilities. > > Herman > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix > Frolow > Sent: Thursday, November 08, 2012 10:36 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] low-resolution and zinc > > Yogi, > I was not mentioning MY book, it is not written yet :-) > Zn an Ca are different element. Zn is transition element 24'th most abundant > on earth, and Ca is alkaline element 5 most abundant on earth. > But in the case of affinity to very strong binding site they behave similarly > - they are picked by the molecule from the surrounding even if they are > present in very low concentrations. > > Beeng in your position I will stop refinement and will take time to define > space group properly. Difference P43 and P43212 (forget about screw axes - > the point groups are important - P4 or P422) > MUST be visible during data processing. If you did not inherited your data > from the source going back in time and collected them (data) by yourself, > difference between merging your data in P4 > or P422 will be VERY visible. If the difference between them is negligible ( > Rmerge factors say 0.04 in one case and 0.05 in another) you have space group > P422 (or merohedral twinning in P4, I can't think clearly in this time of > the day if such twinning is possible). If your space group is P4 and you try > to merge it in space group P422, your Rmerge will be 0.4 -0.5. > Generally, elegant practice of crystallography does not require determination > of the space group using PHASER or MOLREP :-\ These facilities were inserted > into molecular replacement programs for younger generation who come to > protein crystallography with 0 (zero) of mathematics and physics and are > surrounded by similar flock. > In the moment you will know what your space group is and you will know if the > twinning is present, you can concentrate only on refinement. In your case > (3.4 Angstrom resolution) you will find DEN extremely useful. > 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 8, 2012, at 05:27 , SD Y <ccp4...@hotmail.com> wrote: > >> Dear Prof. Frolow, >> >> Our library has that book and I will look read it. I will also look in to >> your book too. >> I haven't been able to differentiate between P43 and P43 21 2, all refining >> results in similar numbers. P43 is slightly better with R work/Rfree is >> 30.5/37%. But its stuck there. >> I have built everything except Zn co-ordination. I will read your chapters >> to learn about SG. >> I understand that Zn is same as Ca as you are suggesting. >> I will also follow the other suggestion you have made regarding Anomolous >> signal. >> >> I sincerely appreciate your time and help which I was very much in need of. >> >> Thanks >> Yogi >> >> From: mbfro...@post.tau.ac.il >> Subject: Re: [ccp4bb] low-resolution and zinc >> Date: Wed, 7 Nov 2012 23:35:35 +0200 >> To: ccp4...@hotmail.com >> >> It is THE BOOK published in 1976! There is a chapter about determination of >> a space group (actually speaking enantiomeric >> space groups such as P3121 or P3112). But it can be expanded to anything, as >> in Blandell (and mine) times we have used to take so called presses ion >> phortographs from which the space groups where easily and swiftly determined >> and only so called enantiomorphic space groups remained elusive…. >> As far as Zn is concerned I am talking about traces. We work with calcium >> binding proteins and never add calcium. Calcium is >> taken from who knows where, but it is there, in the binding site. We >> actually know where from - from traces of the elements. >> As I believe it can be anything. >> FF >> 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 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 >
