The experiment should be very problematic if I can't determine point group on the base of the symmetry merging statistics. Watch CHI2 :-) 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 14:29 , herman.schreu...@sanofi.com wrote: > Then we agree. I got confused because you mentioned"space group" and not > "point group" in your phrase about PHASER and MOLREP and was afraid others > might have gotten confused as well. Also, in case of twinning or almost > crystallographic non-crystallographic symmetry, determining the point group > on the basis of processing statistics alone can be inconclusive or even > misleading. If I recall correctly, there has recently been a thread about > this in the bulletin board. > Herman > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix > Frolow > Sent: Thursday, November 08, 2012 1:14 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] low-resolution and zinc > > 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 >> >
