James S. Defever

All Publications

• A high-throughput energy-dispersive tender X-ray spectrometer for shot-to-shot sulfur measurements. Journal of synchrotron radiation Abraham, B., Nowak, S., Weninger, C., Armenta, R., Defever, J., Day, D., Carini, G., Nakahara, K., Gallo, A., Nelson, S., Nordlund, D., Kroll, T., Hunter, M. S., van Driel, T., Zhu, D., Weng, T. C., Alonso-Mori, R., Sokaras, D. 2019; 26 (Pt 3): 629–34

  Abstract

  An X-ray emission spectrometer that can detect the sulfur Kalpha emission lines with large throughput and a high energy resolution is presented. The instrument is based on a large d-spacing perfect Bragg analyzer that diffracts the sulfur Kalpha emission at close to backscattering angles. This facilitates the application of efficient concepts routinely employed in hard X-ray spectrometers towards the tender X-ray regime. The instrument described in this work is based on an energy-dispersive von Hamos geometry that is well suited for photon-in photon-out spectroscopy at X-ray free-electron laser and synchrotron sources. Comparison of its performance with previously used instrumentation is presented through measurements using sulfur-containing species performed at the LCLS. It is shown that the overall signal intensity is increased by a factor of 15. Implementation of this approach in the design of a tender X-ray spectroscopy endstation for LCLS-II is also discussed.

  View details for DOI 10.1107/S1600577519002431

  View details for PubMedID 31074425

• Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography STRUCTURE Roessler, C. G., Agarwal, R., Allaire, M., Alonso-Mori, R., Andi, B., Bachega, J. F., Bommer, M., Brewster, A. S., Browne, M. C., Chatterjee, R., Cho, E., Cohen, A. E., Cowan, M., Datwani, S., Davidson, V. L., Defever, J., Eaton, B., Ellson, R., Feng, Y., Ghislain, L. P., Glownia, J. M., Han, G., Hattne, J., Hellmich, J., Heroux, A., Ibrahim, M., Kern, J., Kuczewski, A., Lemke, H. T., Liu, P., Majlof, L., McClintock, W. M., Myers, S., Nelsen, S., Olechno, J., Orville, A. M., Sauter, N. K., Soares, A. S., Soltis, S. M., Song, H., Stearns, R. G., Tran, R., Tsai, Y., Uervirojnangkoorn, M., Wilmot, C. M., Yachandra, V., Yano, J., Yukl, E. T., Zhu, D., Zouni, A. 2016; 24 (4): 631-640

  Abstract

  X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.

  View details for DOI 10.1016/j.str.2016.02.007

  View details for Web of Science ID 000373568700019

  View details for PubMedID 26996959

• The X-ray Pump-Probe instrument at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Chollet, M., Alonso-Mori, R., Cammarata, M., Damiani, D., Defever, J., Delor, J. T., Feng, Y., Glownia, J. M., Langton, J. B., Nelson, S., Ramsey, K., Robert, A., Sikorski, M., Song, S., Stefanescu, D., Srinivasan, V., Zhu, D., Lemke, H. T., Fritz, D. M. 2015; 22: 503-507

  Abstract

  The X-ray Pump-Probe instrument achieves femtosecond time-resolution with hard X-ray methods using a free-electron laser source. It covers a photon energy range of 4-24 keV. A femtosecond optical laser system is available across a broad spectrum of wavelengths for generating transient states of matter. The instrument is designed to emphasize versatility and the scientific goals encompass ultrafast physical, chemical and biological processes involved in the transformation of matter and transfer of energy at the atomic scale.

  View details for DOI 10.1107/S1600577515005135

  View details for Web of Science ID 000353920300007

  View details for PubMedID 25931060

  View details for PubMedCentralID PMC4416667

• High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography SCIENCE Boutet, S., Lomb, L., Williams, G. J., Barends, T. R., Aquila, A., Doak, R. B., Weierstall, U., Deponte, D. P., Steinbrener, J., Shoeman, R. L., Messerschmidt, M., Barty, A., White, T. A., Kassemeyer, S., Kirian, R. A., Seibert, M. M., Montanez, P. A., Kenney, C., Herbst, R., Hart, P., Pines, J., Haller, G., Gruner, S. M., Philipp, H. T., Tate, M. W., Hromalik, M., Koerner, L. J., van Bakel, N., Morse, J., Ghonsalves, W., Arnlund, D., Bogan, M. J., Caleman, C., Fromme, R., Hampton, C. Y., Hunter, M. S., Johansson, L. C., Katona, G., Kupitz, C., Liang, M., Martin, A. V., Nass, K., Redecke, L., Stellato, F., Timneanu, N., Wang, D., Zatsepin, N. A., Schafer, D., Defever, J., Neutze, R., Fromme, P., Spence, J. C., Chapman, H. N., Schlichting, I. 2012; 337 (6092): 362-364

  Abstract

  Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  View details for DOI 10.1126/science.1217737

  View details for Web of Science ID 000306542600057

  View details for PubMedID 22653729