[ccp4bb] Postdoctoral position in macromolecular crystallography, HZI Braunschweig, Germany

[Wulf Blankenfeldt]

Postdoctoral Position in Macromolecular Crystallography

The Helmholtz Centre for Infection Research (HZI) in Braunschweig (Germany) 
announces an opening for a postdoctoral researcher in macromolecular 
crystallography. The position is associated with the department “Structure and 
Function of Proteins” headed by Prof. Wulf Blankenfeldt. The department focuses 
on unraveling molecular mechanisms of uncharacterized processes in the 
metabolism, regulation and virulence of pathogenic microorganisms.


About the institute
More than 800 people work at the HZI, a research institution in the Helmholtz 
Association of German Research Centres funded jointly by the Federal Republic 
of Germany and the Federal State of Lower Saxony. The centre’s task is to 
undertake biomedical research in the field of infection biology to expand 
knowledge of the fundamental mechanisms behind medically relevant infectious 
diseases with the aim of providing the key for the development of new 
therapeutics and vaccines.
The Department “Structure and Function of Proteins” offers excellent working 
conditions, state-of-the-art technical platforms and equipment (including 
bacterial, insect cell and mammalian protein expression systems; access to a 
rotating anode X-ray source and several synchrotrons, crystal imaging and 
liquid handling systems; biophysical characterization of proteins), a lively 
scientific community and excellent support for the development of personal 
soft-skills.

Projects
All projects in our department aim at the identification and elucidation of the 
molecular function and mechanism of uncharacterized genes in pathogenic 
microorganisms. A better understanding of these “white spaces” of the genome 
map will not only unravel interesting new molecular processes but also provide 
novel targets for pharmaceutical intervention. To achieve our goal, we employ a 
gamut of methods including – in addition to structural biology – 
microbiological, biophysical and metabolomic techniques.
Because our department is also the prime partner for structural biology-related 
questions at the HZI, the Technical University of Braunschweig and the German 
Centre for Infection Research (http://www.dzif.de/en/) the successful candidate 
will have the opportunity (and is expected) to take leading roles within our 
existing and emerging collaborations.

Prerequisites
Candidates should hold a Ph.D. in a life sciences related subject at the time 
of their employment. They should have a strong background in all aspects of 
macromolecular crystallography, including techniques of recombinant protein 
production and biophysical characterization. Experience in handling and 
manipulating pathogenic bacteria (biosafety level 2) is a plus.

The handicapped
Qualified applicants with a disability will be given preference.

Job details
The position is available immediately for three years with a six month 
probation period. Salary is according to level E14 of the collective labor 
agreement for public service (TVöD).

Application details
Candidates are asked to submit a full CV including a publication list, a cover 
letter outlining their interest in this position, a brief summary of current 
and past research experience (max. 2 pages) and contact data of at least two 
referees. All documents and information should be provided in English or German.

Applications should refer to code 05/2014 and be sent by 28.02.2014 to:

Helmholtz Centre for Infection Research
Dept. of Human Resources
Inhoffenstraße 7
38124 Braunschweig
Germany
E-Mail: jobs...@helmholtz-hzi.de

For further information, please contact Prof. Dr. Wulf Blankenfeldt,
phone: +49-531-6181-7000, e-mail: wulf.blankenfe...@helmholtz-hzi.de




Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie

Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
Bundesministerium für Bildung und Forschung
Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für 
Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477

[ccp4bb] Off-topic: ITC - what to buy?

[Wulf Blankenfeldt]

Dear all:

we are looking into buying an isothermal titration calorimeter, but are 
only aware of two manufacturers: TA Instruments and MicroCal (GE 
Healthcare). Are there any more?


Do you have any recommendations (brand, model etc.) for us?

Thanks in advance,


Wulf

--
Prof. Dr. Wulf Blankenfeldt
NW-I, 2.0.U1.09Universitaet Bayreuth
fon:+49-(0)921-55-2427  Lehrstuhl fuer Biochemie
fax:+49-(0)921-55-2432   Universitaetsstrasse 30
e-mail: wulf.blankenfeldt [at] uni-bayreuth.de95447 Bayreuth
web:www.biochemie.uni-bayreuth.deGermany

[ccp4bb] SHELXL eating REFMAC5 waters - whom to trust?

[Wulf Blankenfeldt]

Dear all,

I am blessed/tormented with a 0.8 A data set for a small protein. I 
first refined it using COOT/REFMAC5 until I deemed it done, which meant 
manually adding quite a few water molecules that were weak and a little 
more distant to the protein. R is 10.2%, R-free is 10.8%.


I realize that referees will probably ask for a SHELXL refinement, so I 
spent the last few days learning about FVAR and SUMP instructions and 
the like and finally got it running in a way I thought should be 
correct. Using my final REFMAC5 model, I get R=10.8% and R-free=11.1% - 
I can certainly live with this, but:


When I now look at the electron density, a large number of my tenderly 
curated water molecules have lost their 2FO-FC electron density (50 out 
of 200; I usually use a 1 sigma cutoff), or they have shifted to lie 
beside a density blob. It may have to do with the fact that I assigned 
0.5 occupancy to some of them and now they have been BUMPed away, others 
may simply be too weak to stay in place.


I wonder what to do now. Do I have to rebuild the water structure again 
and refine everything in SHELXL exclusively? Or are there any flags I 
could use to keep the old waters intact (risking higher R-factors)?


Any help is highly appreciated!

Thank you in advance,


Wulf

[ccp4bb] Making really good chemically competent cells

[Wulf Blankenfeldt]

Dear all,

please excuse the non-CCP4-related question, but maybe there is someone 
out there who can help us.


We are trying to find a recipe for making REALLY good chemically 
competent E. coli for our local cloning facility. What we would like to 
have is more or less:


- 109 cfu/ug DNA
- blue/white selection
- phage resistance
- chemical competence (heat shock transformation)

Our best local methods achieve only about 5*106 cfu, which is too little 
for the cloning method we use.


Any suggestions are highly appreciated.

Thanks in advance,



Wulf