Another question:
since during data collection the chlorine disappears, can the residues
surrounding the chlorine adjust their position to compensate for the
vanishing of the atom? Can the ligand move? Do things move during data
collection?
Meaning, can I describe what I see in my structure as a
But you can change it with the keyword
anomolous formfactor f' f''
Where f' and f'' correspond to values for a given wavelength.
See for details:
http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html
Internally yes. It is CuKa.
Garib
On 29 Nov 2007, at 23:19, Tadeusz Skarzynski wrote:
Dear Elisabetta,
Which program did you use for refinement?
If you used REFMAC, the atomic scattering factors are internally coded for
copper radiation, and the resulting electron density map after refinement
may be much lower for halide atoms than it should be!
It is a known REFMAC issue.
Tadeusz
Thank you for all the answers I am starting to get!
In the meantime, could I please also ask you to suggest to me papers that
would be a good reference to put in my publication?
Thank you again!
Eli =)
On Thu, November 29, 2007 4:21 pm, Fischmann, Thierry wrote:
> Dear Eli,
>
> I work in a pharma
Dear all,
I am refining two structures which have in the active site a ligand
containing a covalent bond between a carbon and a chlorine atom.
I collected the data at APS, SERCAT ID-22.
Because of radiation damage I tried different occupancy values for the
chlorine atom and structure number #1 i
Nonredundant summary - thx to all submitters:
1) disulfide was often present even after expression in a normal BL21 strain
2) try OrigamiB (DE3), Rosetta-Gami 2 from Novagen, are codon optimized and
have mutations in the thiorodoxin reductase and glutathione reductase
genes
- expressing from p
Karen,
MolSoft offers a free online tool that predicts protein-protein
interfaces using our ICM software.
http://www.molsoft.com/oda.cgi
more information here:
http://www.molsoft.com/oda.html
Fernandez-Recio, J., Totrov, M., Skorodumov, C., Abagyan, R.Optimal
Docking Area: A New Method for Pr
To all interested parties:
A Research Scientist / X-ray lab manager position in the lab of Tom
Cech in Boulder, Colorado is open.
Job Description:
The Howard Hughes Medical Institute, a leading biomedical research
organization, is seeking an experienced scientist to manage our X-ray
crys
PhD in GPCR Signalling
In my laboratory at the MRC Laboratory of Molecular Biology there are
PhD opportunities in structural biology of G protein coupled receptor
(GPCR) signalling.
We have outstanding expertise in 2D and 3D crystallisation of GPCRs.
We are working on the structure of GPCR
PISA gives a good analysis of a known interface, but won't predict it
from scratch. So basically you need a protein-protein docking program of
which there are several:
3DDock, gramm, zdock, etc, etc
There's a review in G.R.Smith and MJE Sternberg, Curr Opion Struct Biol,
12, 28 (2002) - obviously
Hi Andreas,
This maybe a little ott, but the Rosetta suite of modelling programs will do
docking with some minimisation and side chain optimisation. You can also
enforce symmetry.
http://www.rosettacommons.org/
http://depts.washington.edu/bakerpg/
It is free to academics and runs on most platfor
Dear all,
Karen question reminded me that I have one also.
I study a protein that homodimerizes via a long helix. A number of
homologs exist. They all dimerize, but the structure is only known of
the first. Homology is high enough that I can easily thread the
homologs' sequences onto the s
HADDOCK..?
protein-protein docking..
Dominguez et al., 2003, JACS, 125, 1731-1737
Kristof
On 29 Nov 2007, at 13:22, karen yates wrote:
Hi,
I would like to find a bioinformatic tool that will allow me to
predict the
dimerisation interface of a protein.
A structural model has been genera
Hey Karen,
Pisa analyzes oligomerization interfaces.
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Andreas
karen yates wrote:
Hi,
I would like to find a bioinformatic tool that will allow me to predict the
dimerisation interface of a protein.
A structural model has been generated, and
Hi,
I would like to find a bioinformatic tool that will allow me to predict the
dimerisation interface of a protein.
A structural model has been generated, and it is known to exist as a homo-dimer.
Does anyone know of a suitable program?
Thank you for your help.
Karen
--
STRUCTURAL BIOLOGY OF WOUND HEALING
A 2 year postdoctoral position, funded by the French National
Research Agency, is available at the Institut de Biologie et Chimie
des Protéines in Lyon (www.ibcp.fr) to study the molecular mechanisms
of wound healing and to develop novel anti-scarring str
POSTDOCTORAL POSITION IN PROTEIN COMPLEX
CRYSTALLOGRAPHY
Applications are invited for a postdoctoral position in Prof. Miquel Colls
group at the Institute for Research in Biomedicine / Institut de Biologia
Molecular de Barcelona (CSIC) to work on the structural
Dear all,
is anyone using the MVE Bio-Medical IATA/CryoShipper for sending crystals by
courier? If you do so, would you please tell me whether it is any good --
especially compared to those others that are more common (e.g. SC 4/2V, CX
100 or similar).
Thank you very much,
Dirk.
---
Dr. DIR
Post-doctoral research position in the Core Program Structural Biology and
Biophysics
Our group is interested in the molecular mechanisms of solute translocation
across bacterial
membranes as well as of c-di-GMP signaling. Based on the molecular structures
that we determine
by X-ray crystallo
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