Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Sep 1;29(Pt 5):1141-1151.
doi: 10.1107/S1600577522007895. Epub 2022 Aug 17.

Fixed-target serial crystallography at the Structural Biology Center

Darren A Sherrell  1 , Alex Lavens  1 , Mateusz Wilamowski  2 , Youngchang Kim  1 , Ryan Chard  3 , Krzysztof Lazarski  1 , Gerold Rosenbaum  1 , Rafael Vescovi  3 , Jessica L Johnson  4 , Chase Akins  4 , Changsoo Chang  1 , Karolina Michalska  1 , Gyorgy Babnigg  4 , Ian Foster  3 , Andrzej Joachimiak  1
Affiliations

Fixed-target serial crystallography at the Structural Biology Center

Darren A Sherrell et al. J Synchrotron Radiat. .

Abstract

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

Keywords: X-ray free-electron lasers; fixed-target serial synchrotron crystallography; structural biology.

PubMed Disclaimer

Figures

Figure 1
Figure 1
ALEX mesh-holder (larger size). (a) Cut-away view of the mesh-holder, (b) expanded isometric view (without magnets) and (c) isometric view of the mesh-holder loading plate.
Figure 2
Figure 2
Setup of ALEX at the 19-ID beamline (a) using a modular magnetic mount prior to permanent integration onto the goniostat (used in data collection reported here), and (b) schematic of permanent integration onto the goniostat with upgraded configuration.
Figure 3
Figure 3
Data collection and processing pipeline. Data captured at 19ID trigger a Globus Flow to transfer images to Argonne Leadership Computing Facility where they are analyzed using the Theta supercomputer (Vescovi et al., 2022 ▸). Results are visualized and published to a searchable data portal for review.
Figure 4
Figure 4
Diffraction patterns obtained from crystals of (a) L1 and (b) DBL. The arrows point to reflection at the indicated resolution.
Figure 5
Figure 5
Room-temperature SSX crystal structures of class B and D β-lactamases. (a) Crystal structure of DBL from C. pinensis determined at 1.80 Å. (b) Crystal structure of class L1 MBL from S. maltophilia determined at 1.85 Å. 2mF o − DF c electron density maps calculated for active sites of C. pinensis DBL (c) and L1 MBL (d). Difference electron density maps contoured at the 1.2σ level.
See this image and copyright information in PMC

References

    1. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. & Zwart, P. H. (2010). Acta Cryst. D66, 213–221. - PMC - PubMed
    1. Ananthakrishnan, R., Blaiszik, B., Chard, K., Chard, R., McCollam, B., Pruyne, J., Rosen, S., Tuecke, S. & Foster, I. (2018). Proceedings of the Practice and Experience on Advanced Research Computing (PEARC’18), 22–26 July 2018, Pittsburgh, PA, USA, pp. 1–7.
    1. Babnigg, G., Sherrell, D., Kim, Y., Johnson, J. L., Nocek, B., Tan, K., Axford, D., Li, H., Bigelow, L., Welk, L., Endres, M., Owen, R. L. & Joachimiak, A. (2022). Acta Cryst. D78, 997–1009. - PMC - PubMed
    1. Babuji, Y., Woodard, A., Li, Z., Katz, D. S., Clifford, B., Kumar, R., Lacinski, L., Chard, R., Wozniak, J. M., Foster, I., Wilde, M. & Chard, K. (2019). Proceedings of the 28th International Symposium on High-Performance Parallel and Distributed Computing (HPDC’19), 22–29 June 2019, Phoenix, AZ, USA, pp. 25–36.
    1. Beyerlein, K. R., Dierksmeyer, D., Mariani, V., Kuhn, M., Sarrou, I., Ottaviano, A., Awel, S., Knoska, J., Fuglerud, S., Jönsson, O., Stern, S., Wiedorn, M. O., Yefanov, O., Adriano, L., Bean, R., Burkhardt, A., Fischer, P., Heymann, M., Horke, D. A., Jungnickel, K. E. J., Kovaleva, E., Lorbeer, O., Metz, M., Meyer, J., Morgan, A., Pande, K., Panneerselvam, S., Seuring, C., Tolstikova, A., Lieske, J., Aplin, S., Roessle, M., White, T. A., Chapman, H. N., Meents, A. & Oberthuer, D. (2017). IUCrJ, 4, 769–777. - PMC - PubMed

LinkOut - more resources