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AK1 Biological Structures

Newsletter December 2010

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Damstadtium Congress CenterMeetings 2010

ECM 26 Darmstadt

The 26th European Crystallographic Meeting was organized this year in Darmstadt, where the large modern Congress Center Darmstadtium provided a perfect venue for the large number of sessions and exhibitions of the conference. There were more than 13 microsymposia organized, which were of large interest for the biological community, sometimes even in parallel sessions. As usual, method-oriented sessions and talks were very well visited.  These included the Monday morning session on "Microcrystals an synchrotron in life sciences"  or the session on "Experimental phasing in structural biology, phase improvement and refinement". In this session, Isabel Usón presented new results and developments of her ab initio phasing program ARCIMBOLDO, followed by Paul Adams presenting new tools for structure refinement in Phenix. In the last talk of this session, Manfred Weiss presented an up to date summary of the use of sulfur SAD for phasing macromolecular structures. Overall, ECM 26 was a well organized and stimulating meeting.

Schoeneck

Meetings 2010

The HEC community meets at Schöneck

by Mariusz Jaskolski (Poznan)
The community of macromolecular crystallographers in central Europe may be of a rather recent vintage but it certainly has its individuality and… a unique tradition. The young protein crystallographers in the Heart of Europe have been gathering each year in the end of September for the now quite famous HEC – or Heart of Europe bio-Crystallography – Meetings. The HEC-13 Meeting (www.uni-leipzig.de/~straeter/hec13) in 2010 (September 23-25), organized in a large conference hotel and vacation resort (Ferienpark) in the charming town of Schöneck located on the rolling hills of Vogtland (Germany), assembled 121 participants from protein crystallography labs in Germany, Poland, the Czech Republic and Austria. The size of the HEC community has grown from 9 groups at HEC-1 (1998) to 22 groups at HEC-13. Even this simple statistics shows that the idea behind the HEC initiative, i.e. fostering protein crystallography in the region, is really bearing fruit. But even more spectacular is the ever increasing scientific level of the Meetings.

The 26 talks delivered by the participants (mostly by students, PhD students and young postdocs) were of veryHEC13 group photo high quality, both with regard to scientific content and the form of presentation. The HEC Prize commission had, therefore, a very hard job to select the best student presentation. Finally, the award went to Bernd Gardill (University of Erlangen) who presented a paper “Don’t behave like a rat: Corticosteroid-binding globulin and the serpin S->R transition”. The second prize, both sponsored by the IUCr, was awarded to Ulrike Bräuer (MLU Halle) for her contribution on “Structural studies of the aminotransferase LivB”. Another surprise was the quality and liveliness of the discussions that followed all the talks, without exception. The atmosphere of the discussions, dominated by the voices of the younger participants, was very skillfully set by Udo Heinemann who chaired the first session. Group leaders are allotted time only to briefly introduce new groups. This year, Markus Wahl presented the research profile of his team at Free University of Berlin and Mikio Tanabe introduced himself as a junior group leader at Martin Luther University (Halle). Three other groups, from the Max-Delbrück-Center (Berlin), the International Institute of Molecular and Cell Biology (Warsaw) and Humboldt University (Berlin), already present at HEC-13, will be introduced by their leaders at HEC-14. The HEC program traditionally includes a special HEC Lecture, delivered by a key methods developer or a scholar of high reputation in our field. The HEC-13 Lecturer was Alexander Popov from the ESRF, who presented a very interesting lecture on practical aspects of diffraction data quality, with emphasis on radiation damage effects.

The Meeting was organized in a perfect manner by Norbert Sträter and his team. Special thanks for a job well done go to Christian Roth, Bartholomeus Küttner and Gabriele Büttner (secretariat). The HEC-13 program offered an excursion to a space travel museum, an alternative hike of the Vogtland hills, or a few relaxing hours in the Ferienpark’s AquaWorld. In summary, the HEC family has had another successful reunion, with lots of excellent science, ample time for exchanging ideas, good atmosphere, good food, and excellent company.

The HEC Committee, which oversees the development of the HEC initiative, has already made a selection for the venue of the 2011 Meeting. HEC-14 (September 29-October 1) will be organized in Żagań (Sagan), to commemorate Johannes Kepler, whose book “De Nive Sexangula” (“On the Six-Cornered Snowflake”) heralded in 1611 the birth of modern crystallography.

Journals and citations

Citations in supplementary material

Publications describing crystallographic methods are frequently cited only the supplementary part of journals such as Nature, Science, Cell or PNAS. These citations are not indexed by the commonly used literature search engines such as PubMed, Scopus, Web of Science or Scholar. As a result the impact factor of journals publishing primarily methodological papers is significantly lower as it should be since the methods part is in the above mentioned journals usually described in the supplementary material.  In a systematic study of ~300 articles published in these journals Weiss et al. [1] found that ~20 %  of all references (main-text and supplementary material) are published in the supplementary material.  The authors find that: "References to IUCr publications, however,  amount to about 8% of all references, but 19% of all references in supplementary material. Further, almost half of all references to publications in IUCr journals end up being published in the supplementary material only. This is bad news for the crystallographic community. Not only does this mean that the impact factor of IUCr journals should be higher, but also that the real overall numbers of citations of methods papers are much higher than what is reported, for instance, by the Web of Science."
The best solution to this problem would probably be that the literature search engines would include the references in supplementary material in the citation statistics, but it is also of utmost importance, that all authors of publications take great care in ensuring proper citation of the works of others.

[1] Manfred S. Weiss, Howard Einspahr, Edward N. Baker, Zbigniew Dauter,
Anke R. Kaysser-Pyzalla, Gernot Kostorz and Sine Larsen J. Appl. Cryst. (2010). 43, 1285–1286

Synchrotron radiation for the life sciences

Representation of the life sciences in the Komitee "Forschung mit Synchrotronstrahlung" (KFS)

by Ullrich Pietsch (Head of the 8th KFS)
In the article (in German language) linked here, the role of the KFS (Komitee für Forschung mit Synchrotronstrahlung" for the coordination and supervision of synchrotron radiation facilities is described, with a particular focus on the role and representation of the life sciences in this committee.
All members of the AK1, who work with synchrotron radiation, should participate in the upcoming elections for the 9th KFS. Until January 2011 candidates can be suggested for the elections in February/March 2011. Further information can be found at www.kfsyn.de

BESSY MX tutorial 2009Crystallographic software

XDSi – A new GUI for processing datasets using XDS

by Michael Krug, Manfred Weiss und Uwe Mueller

XDS [1-3] is a very up-to-date and sophisticated software for processing single-crystal monochromatic diffraction data from macromolecular and other crystals recorded by the rotation method. Time consuming steps such as the collection of strong spots and the integration step are parallelized to take advantage of the multiprocessor architecture of modern computers. Additionally, XDS uses an elaborated 3D profile-fitting algorithm for the integration process. However, XDS is a text-based software, which means that it is hard, especially for unexperienced users, to run the program and to evaluate the quality of the processed dataset. Unfortunately, this often prevents especially students, which are new in the field of MX from using XDS as their main diffraction data processing software.
XDSi is a graphical user interface (GUI) that combines the software packages XDS, POINTLESS of the CCP4 software suite [4] and XDSSTAT [5], allowing the user to index or integrate one or multiple diffraction image data sets with minimum effort. The most probable space group is determined with the help of POINTLESS and additional statistcs are generated by XDSSTAT. A short summary of the indexing as well as the integration step is displayed for each data set. During integration, the most important statistics (e.g scale factors, mosaicity, number of strong spots) can be followed “live” (see figure). All important statistics are stored as plots in a single pdf file. This file also includes statistics generated by XDSSTAT like the redundancy-independent merging R-factor Rmeas/Rr.i.m. per frame that can be used to identify images of the dataset that are of much poorer quality than the rest of the dataset, or the decay R-factor RD [5] giving information about the occurrence of radiation damage in the crystal during the process of data collection.
XDSi is available and can be used on all HZB-MX beamlines.
 
References
[1] W. Kabsch (1993). Automatic processing of rotation diffraction data from crystals of initially unkown symmetry and cell constants. J. Appl. Cryst. 26, 795-800.
[2] W. Kabsch (2010). XDS. Acta Cryst. D66, 125-132.
[3] W. Kabsch (2010). Integration, scaling, space-group assignment and post-refinement. Acta Cryst. D66, 133-144.
[4] Collaborative Computational Project, The CCP4 suite: programs for protein crystallography (1994). Acta Cryst. D50, 760-763.
[5] K. Diederichs (2006). Some aspects of quantitative analysis and correction of radiation damage, Acta Cryst. D62, 96-101.

BESSY Screening 14.1Data collection

The in situ crystal screening facility at the BESSY-MX beamline 14.1

Karthik S. Paithankar, Michael Hellmig, Ronald Förster, Manfred S. Weiss and Uwe Mueller
Over the past years, new technology developments like automation of expression, purification, and crystallisation have led to an increase of successful structure solutions the field of macromolecular crystallography. Although automated optical imaging has accelerated the pace of the macromolecular crystallisation methods, human efforts are still required to pick individual crystalline specimens from crystallisation plates to identify conditions that give rise to useful X-ray diffraction. During this process, sensitive crystals may get mechanically affected or compromised by non-optimal cryo-protectant solutions. This often leads to poor or no diffraction. An alternative to rapidly identify conditions that show diffractable crystals is, to expose crystals or possible crystalline material grown directly inside crystallisation plates with X-rays [1].
BL14.1 contains a state-of-the-art CATS (Cryogenic Automated Transfer System) robot hardware implementation, which consists of a six-axis robot arm. This arm can handle a dedicated tool that manipulates either crystallisation plates or cryo-cooled samples (Figure 1). Every object within the plate can thus be precisely positioned in front of the X-ray beam. The robot arm acts as the omega-rotation axis during diffraction data collection. The gripper can handle plates most commonly used by the community, which confirm to ANSI/SBS 1-2004 standards.
Different proteins and a DNA-duplex (deoxyoctanucleotide) have been subjected to standard sparse-matrix crystallisation screens and exposed in the X-ray beam using the robot (Figure 2). The method helps in unambiguous identification of crystalline and non-crystalline objects. After a background subtraction filter has been applied, the diffraction images can be auto-indexed and important metrics of the crystal system can be determined. Furthermore, in some favourable cases data sets can be collected.
The in situ screening facility at HZB-MX is now available for external users. You can find detailed information on our website at http://www.helmholtz-berlin.de/bessy-mx/.

IUCr Acta F structural genomicsActa Crystallographica Section F showcases structural genomics publications

by Andrea Sharpe
The application of high-throughput methods to structural biology has generated an abundance of new macromolecular structures. In order to help ease the resultant publication backlog, Acta Crystallographica Section F now offers a special publication strategy to showcase these structures and the experiments upon which they are based. The first example was published in December 2009 and contained eight papers from the RIKEN-UK structural genomics consortium in a special section of the journal.
More recently (October 2010), the journal published a special issue that focuses exclusively on 35 structures, grouped into context, from the Protein Structure Initiative Joint Center for Structural Genomics. The issue, which is open access, is available from http://journals.iucr.org/f/issues/2010/10/00/issconts.html. This milestone publication has been enthusiastically welcomed by the community, and new requests and proposals for further special issues and special sections are under consideration.

First crystal structure of a eukaryotic ribosome

Following crystal structure determination of bacterial ribosomes, Ben-Shem et al. now present the first X-ray structure of a eukaryotic ribosome, determined at 4.15 Angstrom resolution for the yeast 80S ribosome. Eukaryotic ribosomes are 40% larger than their bacterial counterparts. Fast and gentle purification techniques were crucial in obtaining crystals suitable for structural studies.

http://www.sciencemag.org/content/330/6008/1203.full
http://www.nature.com/news/2010/101125/full/news.2010.632.html

HZB user meeting at Bessy II

The HZB (Helmholtz Zentrum Berlin) annual user meeting was organized on December 9 and 10 at Bessy II. With 27 posters, the macromolecular crystallography community was fairly well represented. For the first time, a poster from MX won the BESSY poster prize. Out of 250 posters in total, the poster by Dirk Roeser from Jena was selected as the champion poster. In addition, Ulrike Krug from Leipzig won the BESSY-MX poster prize.

We wish all of you nice holidays and a good start into a happy and successful new year!

Calender/Meetings

05.01.-07.01.2011 CCP4 study weekend, Warwick, UK
GRK1026 Logo
03.03.- 05.03.2011
2nd International Meeting "Conformational transitions in macromolecular interactions", Halle, Germany
22.08.-30.08.2011
IUCr 2011, Madrid
20.09.-24.09.2011 DGK-Meeting 2011, Salzburg
29.09.-01.10.2011 HEC-14, Sagan, Poland
Impressum/Contact
The AK1 Newsletter is published by the working group "Biological Structures" of the Deutsche Gesellschaft für Kristallographie (DGK) and the Gesellschaft für Biochemie und Molekularbiologie (GBM) study group "Structural Biology" by the following editors:
Norbert Sträter (strater@bbz.uni-leipzig.de)
Manfred Weiss (msweiss@helmholtz-berlin.de)
Ralf Ficner, Spokesman AK1 (rficner@gwdg.de)
Yves Muller, Vice Spokesman AK1, (ymuller@biologie.uni-erlangen.de)
Roman Hillig, Bayer HealthCare Pharmaceuticals (roman.hillig@bayer.com)
Dirk Heinz, Spokesman of the study group structural biology of the GBM (Dirk.Heinz@helmholtz-hzi.de)

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