[ccp4bb] Research Technician Position in University of Vienna, Austria

[Kristina Djinovic Carugo]

*Research technician position *
is available in the research *group of Kristina Djinovic-Carugo* in the 
Department for Structural and Computational Biology, Max. F. Perutz 
Laboratories of the University of Vienna, Austria. The main area of the 
group research is structural biology of F-actin based cytoskeleton, with 
main focus on striated muscle. The lab uses an integrative structural 
biology approach combining biophysical and high resolution structural 
studies (macromolecular crystallography being the main technique) with 
lower resolution approaches (SAXS, SANS, EM) or specific distance 
information (chemical cross-linking coupled to mass-spectrometry, NMR).


The Department for Structural and Computational Biology is equipped with 
state of the art instrumentation/facilities to carry out all steps from 
cloning, protein expression and purification, to X-ray diffraction, 
biomolecular NMR, as well as for a series of biophysical and optical 
spectroscopy techniques. The Department is located on Vienna Campus 
Biocenter, which is the largest life sciences hub in Austria. Vienna is 
frequently ranked the world’s best city to live in. It is a United 
Nations city with a large English-speaking community.


*Job Responsibilities*

You will be assisting in the lab on a variety of biochemical and 
biophysical studies, including gene cloning, protein expression, 
purification, and characterization of purified protein by various 
biochemical and biophysical techniques, and protein crystallization. You 
are also expected to help with management of laboratory, together with 
lab-manager of the research group.


*The Candidate*

We are looking for a highly motivated candidate who is enthusiastic to 
work in an ambitious and multidisciplinary team and fits the following 
profile:**


 * Bachelor’s/Master’s degree in Biochemistry, Molecular Biology, or a
   related field
 * Excellent understanding of the theoretical and technical principles
   of common techniques in protein biochemistry and molecular biology,
   such as molecular cloning, protein expression and purification and
   biophysical characterization.
 * Practical experience with molecular biology, molecular cloning
   techniques, protein purification, and biochemistry is essential;
   experience in insect and/or mammalian cell culture is an asset.
 * Experience with protein crystallization, biophysical
   characterization and structure determination will be highly valued.
 * She/He should be willing to acquire further skills and contribute to
   the development of new methods.
 * Excellent command of English (spoken and written) is a must, German
   skills are an asset. Computer literacy and experience of using
   Microsoft Word, Excel and PowerPoint is essential.

*Application details*: if you want to join an exiting project and become 
a member of our interdisciplinary team please compile an application 
package containing:


 * Letter of interest
 * Your CV
 * Contact details for two references

and submit your application to *Kristina Djinovic Carugo *(to /e-mail: 
*admin.v...@univie.ac.at*/) by *March 12^th , 2017.*


This is a full-time post for up to 2 years with the possibility for 
extension to max 7 years subject to successful evaluation. The post is 
funded by the Christian Doppler Laboratory for High‐Content Structural 
Biology and Biotechnology and is available for immediate start.


Brutto salary for 40 hours/week is EUR 2023,40.


--
Department of Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Vienna Biocenter (VBC), Campus Vienna Biocenter 5
A-1030 Vienna
Austria


e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203
Phone: +43-1-4277-52201 (secretary)
Mobile A: +43-664-602 77-522 03
Fax: +43-1-4277-9522

Re: [ccp4bb] How to convince oneself (and others) of ligand presence

[Frank von Delft]

PanDDA tries to arrive at an objective score metric for presence:

http://biorxiv.org/content/early/2016/09/05/073411

But in the end, you still have to apply all the scientific rigour that 
Bernard mentions.



On 23/02/2017 13:56, Mohamed Noor wrote:

Dear all

I think I have a ligand (substrate) placed in the active site of my model 
correctly. The CC is 0.785, B factor of 60 A^2 which is roughly similar to the 
neighboring residues and there was no ligand in my search model*. The data 
extends to 2.2 A, although I think I can get something higher with manual 
processing**. How can I be really sure that it is the ligand that I think it 
is? And assuming you are a reviewer, what would you expect to see in a 
manuscript?

* The unliganded model was obtained by molecular replacement using a search 
model that did not have the ligand. I then used this model to simply do one 
cycle of rigid-body refinement and another one cycle of coordinate/ADP 
refinement.

** The data was auto-processed during data collection using xia2/XDS. I have a 
dozen of datasets so I am just taking the autoprocessed ones and see if my 
ligand is there.

Thanks.
Mohamed

Re: [ccp4bb] intermolecular dissulphides

[Johannes Cramer]

Dear Eleanor,

sorry for the late reply. I found a similar case (id: 2OEF, Cys 92). I
mutated the Cys to Ser, but it did not change anything (xtal conditions and
quality remained the same). In solution the protein is a monomer.
However, adding 1 mM DTT resulted in a significant increase in crystal
quality (larger 3D crystals with better resolution). I don't know why,
though...

Cheers,
Johannes

2017-02-01 20:45 GMT+01:00 Tom Peat :

> Hello Eleanor,
>
>
> We found some intermolecular vicinal disulfides recently that we think are
> 'real'. This class of proteins forms tetramers and in one version we find
> these intermolecular disulfides across molecules. We did some tests and
> found that oxidation or reduction has an effect on the stability of the
> protein. ​We also saw this was consistent across multiple space groups. If
> you would like to have a look, they were just released: 5HY0, 5HY2, 5HY4.
>
> As a comparison to another protein in this fold class that doesn't have
> the disulfide is 5HWE.
>
>
> cheers, tom
>
>
> Tom Peat
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304 <+61%203%209662%207304>
> +614 57 539 419
> tom.p...@csiro.au
> --
> *From:* CCP4 bulletin board  on behalf of Eleanor
> Dodson 
> *Sent:* Thursday, February 2, 2017 2:17 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] intermolecular dissulphides
>
> Does anyone know of examples of these?
> I have found one - 2WQW with these SSBOND records
> 2WQW
> SSBOND   1 CYS A  206CYS A  227  1555   6556
> 2.07
> SSBOND   2 CYS B  206CYS B  227  1555   5556
> 2.15
>
> We seem to have one but it would have to form after crystalisation?
>
> Eleanor
>
>
>

[ccp4bb] How to convince oneself (and others) of ligand presence

[Mohamed Noor]

Dear all

I think I have a ligand (substrate) placed in the active site of my model 
correctly. The CC is 0.785, B factor of 60 A^2 which is roughly similar to the 
neighboring residues and there was no ligand in my search model*. The data 
extends to 2.2 A, although I think I can get something higher with manual 
processing**. How can I be really sure that it is the ligand that I think it 
is? And assuming you are a reviewer, what would you expect to see in a 
manuscript?

* The unliganded model was obtained by molecular replacement using a search 
model that did not have the ligand. I then used this model to simply do one 
cycle of rigid-body refinement and another one cycle of coordinate/ADP 
refinement.

** The data was auto-processed during data collection using xia2/XDS. I have a 
dozen of datasets so I am just taking the autoprocessed ones and see if my 
ligand is there.

Thanks.
Mohamed

[ccp4bb] postdoc fellowships available: in vitro reconstitution and cryo-EM

[Lars-Anders Carlson]

Dear all,
Two postdoc fellowships are available in my lab at Umeå University, 
Sweden. The projects aim to decipher the molecular basis of human RNA 
virus replication using in vitro membrane reconstitution and cryo-EM 
(tomography of cells and single particle analysis).


We are looking for highly motivated candidates with a background in 
structural biology, biophysics, biochemistry or a related field. While 
prior knowledge of cryo-electron microscopy or in vitro reconstitution 
is beneficial, these are the core methods of the lab and we can thus 
also provide a postdoc with in situ training specific to the project. 
These projects may be a great opportunity for candidates with a 
background in X-ray crystallography who want to expand their 
methodological scope.


Umeå has just completed the installation of a new cryo-EM facility 
including a Titan Krios with a phase plate, energy filter and two direct 
detectors, a Scios FIB/SEM and a Talos 120. Resources for biochemistry 
and fluorescence microscopy are also excellent. Umeå is an outstanding 
environment for molecular infection biology, including the Nordic EMBL 
Node MIMS and the Wallenberg Centre for Molecular Medicine.


For more information about the projects and how to apply, got to
http://www.ucmr.umu.se/positions.html

Feel free to contact me directly with any questions!

Best wishes,
Lars


--
Lars-Anders Carlson, Dr. rer. nat.
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Umeå University

http://www.medchem.umu.se/english/research/principal-investigators/lars-anders-carlson/

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2017

[Manfred S. Weiss]

Please mark your calendar:

The next MX-proposal application deadline: March 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2017-01/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: Goniometer upgrade of BL14.1

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with over 300 PDB depositions annually. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- PILATUS 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
  (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- PILATUS 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please visit
http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/fragment-screening/index_en.html
or contact us at 
mswe...@helmholtz-berlin.de.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG