> HI
>
> This is an off-topic question. I have recently started working with
> ribosomes.
>
> I do not have any experience as such. Inorder to check whether the ribosome
> I purify is functional, Can anyone please suggest some assay which does not
> require the usage of radioactive material?
>
>
Dear Gerard,
Actually, for some of the tests we turned off the DEN network restraints
for the last two refinement macrocycles, so, at least for these
particular cases, the DEN method truly found a better minimum
rather than forcing the system to the higher resolution structure.
Cheers,
Axel
O
Extrapolating to the infinite, I wonder how super-resolution fits into
MD models or structure predictions?
Jacob
On Thu, Dec 23, 2010 at 5:04 PM, Gerard Bricogne wrote:
> Dear Bernhard,
>
> I must say that I find the "super-resolution" claims in this paper a
> bit of a conjuring trick. If th
Dear Bernhard,
I must say that I find the "super-resolution" claims in this paper a
bit of a conjuring trick. If the final refined model has greater accuracy
than one would expect from the resolution of the data it has been refined
against, it is because that extra accuracy has been lifted fr
Cross-posted from pdb-l
--Gerard
-- Forwarded message --
Date: Thu, 23 Dec 2010 15:35:10 -0500
From: Christine Zardecki
To: pd...@rcsb.org
Subject: pdb-l: From 7 to 70,000: The PDB Reaches a New Milestone
From 7 to 70,000: The PDB Reaches a New Milestone
As the year 2010 dr
> electron density for an atom with a B of 100 Angstroms**2 is so flat
> that you wonder how those atoms can be seen in electron density maps
Hmmthen there would not be any low resolution structures:
Say you have a low resolution structure, 3.5 A with a mean B of ~100A2 or
so.
Then on avera
Oops I am outdated: Axel just emailed me that he describes an improved
coordinate estimate beyond the Rayleigh criterion in his recent paper
Schroder GF, Levitt M, & Brunger AT (2010) Super-resolution biomolecular
crystallography with low-resolution data. Nature 464(7292), 1218-1222.
For the defo
Something related to the results in the 1984 paper, but never published, is
that the calculated electron density for an atom with a B of 100 Angstroms**2
is so flat that you wonder how those atoms can be seen in electron density maps.
Ron
On Thu, 23 Dec 2010, Bernhard Rupp (Hofkristallrat a.D.
> can anyone point me to a more exact theory of distance accuracy compared
to
> optical resolution, preferably one that would apply to microscopy as well.
Stenkamp RE, & Jensen LH (1984) Resolution revisited: limit of detail in
electron density maps. Acta Crystallogr. A40(3), 251-254.
MX, BR
In my experience, either urea or guanidinium crashes out in gels. I
can't remember--which one is it? I am thinking guanidinium. (If the
answer to this email saves one grad student from the aggravation of
such a phenomenon, it will have been worth it...)
It's GuHCl and what crashes is dodecyl su
In my experience, either urea or guanidinium crashes out in gels. I
can't remember--which one is it? I am thinking guanidinium. (If the
answer to this email saves one grad student from the aggravation of
such a phenomenon, it will have been worth it...)
JPK
On Thu, Dec 23, 2010 at 9:31 AM, Preben
This posting concerning positional precision prompted me to recall a
CCP4 meeting (not a recent one) where a well-known crystallographer
(who shall remain nameless - present company excepted BTW - AFAIK the
crystallographer in question has never posted to this BB) claimed that
an atom with a B fact
Hello:
I am making a kinase in e.coli that seems to autophosphorylate itself a bit,
which makes it difficult to get a pure homogeneous sample for crystallization.
I would like to use a phosphatase to remove the abberant phosphorylation. I
have seen lambda phosphatase used for this type of thing
Hi,
you might have a look into the papers of MM Harding. There is a series
of papers about metal ions in X-ray structures in Acta D.
Look at the number of coordination, geometry and distances. Then you can
easily decide whether there is a metal ion and which metal ion it might be.
And of course
Hi Jacob
Why not try with urea and
for this type of studies I would probably use batch with the IMAC resin and not
run the samples over a column.
cheers
Preben
On 23/12/2010, at 16.11, Jacob Keller wrote:
> Dear Crystallographers,
>
> I am interested in doing a type of pull-down experimen
Dear Crystallographers,
I am interested in doing a type of pull-down experiment by
immobilizing protein X on IMAC resin, flowing a large volume of dilute
lysate containing protein Y over it, then adding some concentrated
agent (solid SDS perhaps) to some more of the same lysate, and running
that o
Hi Nick
The 0.1 to 0.3 Ang range you quote obviously only applies to the kind
of atoms we as macromolecular crystallographers are interested in,
i.e. mostly carbon with some nitrogen & oxygen, and also at the
'typical' data resolution and B factors that we observe. For hydrogen
it would obviously
Dear Nick
I think the point here is more the precision achieved via the fitting
of atom positions according to the gradient of the electron density.
There is obviously an overall link of the detail of/in this gradient
to the measurable diffraction resolution, which can be estimated in a
number of w
We clearly have confidence in distance measurements in crystal
structures of an order of magnitude better than the resolution ie
0.1-0.3 Angstroms, but can anyone point me to a more exact theory of
distance accuracy compared to optical resolution, preferably one that
would apply to microscopy a
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