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:[email protected]] On
Behalf Of Felix Frolow
Sent: Thursday, November 08, 2012 1:14 PM
To: [email protected]
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: [email protected]
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Nov 8, 2012, at 12:20 , [email protected] 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:[email protected]] On Behalf Of Felix Frolow
Sent: Thursday, November 08, 2012 10:36 AM
To: [email protected]
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: [email protected]
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Nov 8, 2012, at 05:27 , SD Y
<[email protected]> 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: [email protected]
Subject: Re: [ccp4bb] low-resolution and
zinc
Date: Wed, 7 Nov 2012 23:35:35 +0200
To: [email protected]
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: [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
