[ccp4bb] dry shippers

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.

[ccp4bb] NEW POSTDOCTORAL POSITION IN PROTEIN COMPLEX CRYSTALLOGRAPHY (Barcelona)

POSTDOCTORAL POSITION IN PROTEIN COMPLEX CRYSTALLOGRAPHY Applications are invited for a postdoctoral position in Prof. Miquel Coll’s group at the Institute for Research in Biomedicine / Institut de Biologia Molecular de Barcelona (CSIC) to work on the

[ccp4bb] Postdoc position in Basel

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

[ccp4bb] Protein interface prediction tool?

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

Re: [ccp4bb] Protein interface prediction tool?

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,

[ccp4bb] more on dimerization interface analysis

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

Re: [ccp4bb] Protein interface prediction tool?

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

Re: [ccp4bb] more on dimerization interface analysis

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

Re: [ccp4bb] Protein interface prediction tool?

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) -

[ccp4bb] PhD in GPCR Signalling

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

[ccp4bb] HHMI X-ray lab manager/Research Scientist Job

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

Re: [ccp4bb] Protein interface prediction tool?

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

Re: [ccp4bb] S-S in EC

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

[ccp4bb] Finding Chlorine =)

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

Re: [ccp4bb] Finding Chlorine =)

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

Re: [ccp4bb] Finding Chlorine =)

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.

Re: [ccp4bb] Finding Chlorine =)

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

Re: [ccp4bb] Finding Chlorine =)

But you can change it with the keyword anomolous formfactor element 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