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
