Hello all
I have refined and built model a dataset of 3.0A resolution dataset. This
model is assocaied with a ligand. After final refinement and model building
i found a big blob of Fo-Fc density of around 4sigma level at the
N-terminal of the fianl model. My protein doesnot carry any tag at
Peter from you description seems that big blob is not your ligand. In 3.0
resolution molecules with similar size, including ligands, tend to look
similar in shape as well. I suggest you refine further your structure and
check again later this N-terminal blob of density. It may tern out to be a
Hello Peter,
at 3A resolution occupancy refinement is supposed to fail, I'd say.
The large B-values can make up for reduced occupancy (as you already
pointed out to) but also large flexibility.
You might try ten refinement runs in parallel with fixed occupancies
varying from 10% to 100% and
I guess it depends on your criteria for success. We made a successful MR using
data to 8Å with a search-model with 20% identity covering 90% of the target. The
resultant phases gave a map where a few new 'blobs' could be observed. Not very
useful, but the MR-phases could be used to solve the HA
Dear CCP4BB Members,
Diamond have a number of vacancies, please click on the links below for
details.
Best regards,
Tim Hannon
Diamond Human Resources
01235 778452
Principal Beamline Scientists
http://www.diamond.ac.uk/Jobs/CurrentVacancies/Scientific/DIA0488.htm
Hi,
We had success using a testosterone hemisuccinate derivative which is
much more soluble.
For details, see: Drevelle et al; J Mol Biol. javascript:AL_get(this,
'jour', 'J Mol Biol.'); 2006 Apr 28;358(2):455-71
Hope this helps!!
Marc
KUMARASWAMI MUTHIAH a écrit :
Anybody tried to
Dear ccp4bb,
I'm trying to update Tcl/Tk on a mac running OSX5.6 as my version of
mosflm has suddenly started crashing when trying to autoindex, so I
figured the best thing to do was to reinstall both mosflm and its
dependencies.
So I went to the CCP4 download page and used the Daresbury
On Wed, 2009-04-01 at 14:33 -0700, Ethan Merritt wrote:
On Wednesday 01 April 2009 07:21:16 Thomas Womack wrote:
A perusal of the PDB reveals that the game of Periodic Table bingo still
has eleven rounds to run:
scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium,
Let me start by quoting the following..
/Therefore I'm afraid that we (i.e. PDB) are under considerable
pressure from the community at large to implement our publication policy
in this area.
We do understand your concern to make the entry as accurate as possible./
I love the /under
the program
www.ebi.ac.uk/~henrick/doss.tar.gz
based on promotif will do the angle between helices
(so then will promotif)
doss is f90 so may work with gfortran
--
Kim HENRICKhenr...@ebi.ac.uk ::telephone: +44 (0) 1223 494629
On Apr 2, 2009, at 16:04, mesters wrote:
Let me start by quoting the following..
/Therefore I'm afraid that we (i.e. PDB) are under considerable
pressure from the community at large to implement our publication
policy
in this area.
We do understand your concern to make the entry as
A standard orientation is anything you want it to be and is usually
defined in the context of orthogonal axes. It is simply a reference
point from which you apply the results of your search. We usually
use one or more of the orthogonal axes as a starting point for easier
visualization.
Moving the subject further away from the original post...
I agree that the pdb deposition process has gotten better, but I still
regularly have issues with releasing of newly published structures.
There seem to be delays; just as you are reading this brand new,
interesting structure, you
I do not mind PDB releasing only on Wednesdays at a certain time of the
day. What should happen is the authors/publishers should let PDB know
the publication date before it becomes available (supposedly days or
weeks before the actual publication, online or in print), and PDB can
automatically
Hi,
I am refining a structure and have a region of unmodeled density into
which I am trying to fit a ligand. The identity of the ligand is not
obvious, so I modeled a bunch of dummy atoms into the density.
Could you please have a look at the map and pdb files and help me
identify this ligand?
Some context would be helpful (essential?). What's
in the crystallization solution? What, if anything, is known about the
protein of interest? What is the ligand interacting with (metal ions,
hydrogen bonding donors/acceptors, charged residues, etc?), and what
are the interaction distances? Do
Hi,
I have a crystal grown in 2.1M 1,6 hexanediol/0.1 M tro-sodium citrate (pH 6.5).
What's the cryoprotectant can be used to flash cool this crystal?
Any online protein crystal cryoprotectant database or published literature
available I can check with to determine to type and
My money is on:
Dithiothreitol or dithioerythritol.
Any chance they are in there? If not and you believe this copurified with
your protein, than I'd guess erythritol or threitol.
(I didn't bother trying to gauge the stereochemistry from your picture)
Cheers
Andy
On 4/2/09 1:38 PM, Abhinav
Some more info about this structure:
Crystallization conditions: Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000,
0.1M TRIS pH 8.5
This does not sit on any crystalllographic symmetry axis.
But it sits right between two monomers and the NCS 2-fold axis.
The protein is chemotaxis protein CheX.
The cryoprotectant is 1,6 hexanediol.
Jim
On Thu, 2 Apr 2009, HanJie_Heng Chiat Tai wrote:
Hi,
I have a crystal grown in 2.1M 1,6 hexanediol/0.1 M tro-sodium citrate (pH 6.5).
What's the cryoprotectant can be used to flash cool this crystal?
Any online protein crystal
Hi, Jim,
What's the concentration? I know that [hexanediol] between 2.5 - 3.4 M no
additional cryoprotectant is required.
But in my case my hexanediol conc is only 2.1 M
Rgds,
HengChiat Tai (HanJie)
Date: Thu, 2 Apr 2009 13:11:27 -0500
From: jim.pflugr...@rigaku.com
To:
If you are uncertain, just freeze your buffer :-)
Very old trick from the stone age of crystallography.
Long time ago ~ 1999 I cryoed one crystal with 1.5 M hexanediol but
there was also 10% glycerol around.
Jürgen
On 2 Apr 2009, at 14:56, HanJie_Heng Chiat Tai wrote:
Hi, Jim,
What's the
Hi People,
Could anyone point me to successful examples for two unrelated
proteins that have been stitched together into one single polypeptide
chain with flexible amino acids to create a functional chimera that
was subsequently crystallized. I've looked up a few.
I am particularly
Postdoctoral Position available in the Laboratory of Wim Hol
Department of Biochemistry, School of Medicine,
University of Washington, Seattle, USA
Structural Biology and structure-based inhibitor design of the invasion
machinery of the malaria parasite.
JOB DESCRIPTION:
This project
Looks like oxalate with two water molecules nearby. Oxalate is a fairly
common product of PEG oxidation.
Artem
---
When the Weasel comes to give New Year's greetings to the Chickens no good
intentions are in his mind.
-Original Message-
From: CCP4 bulletin board
I only deposited the high-res apo coordinates, but pdb code 2AU3 was solved
from a thulium soaked crystal. In fact, I also used dysprosium to phase
primase from a different bacterium. Go team lanthanide!
On Wed, 1 Apr 2009 15:21:16 +0100, Thomas Womack twom...@globalphasing.com
wrote:
A perusal
Hi all,
You can find our release policy in the chapter 2 of Annotation
Policies document which is available from the following URL.
http://www.wwpdb.org/docs.html
We encourage all the PDB depositors to carefully check the journal
policy for the availability of coordinates (and experimental
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