Table of Contents

• Acknowledging SSRL Macromolecular Crystallography
• References to supported hardware and software
  • Software
  • Remote access crystallography
  • Advanced instrumentation and methods

Referencing SSRL

The acknowledgement section of publications that are based in part or fully on data collected at the macromolecular crystallography beamlines should contain the following text (as cited in the SSRL publication report page):

Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH.

You are also encouraged to acknowledge your support staff contact person if they provide help during your beamtime. If the support staff make particularly valuable suggestions or contribute in a non negligible way to the sucess of the experiment, you may consider making them coauthors in resulting publications.

It is very important that you tell us about publications relevant to work conducted at SSRL. Please fill out the publication form.

References to supported hardware and software

The following are references of supported hardware and software at SSRL Macromolecular Crystallography. Please use the appropriate references in your publications.

Software

Blu-Ice/DCS Experimental Control: McPhillips, T. M., McPhillips, S. E., Chiu, H. J., Cohen, A. E., Deacon, A. M., Ellis, P. J., Garman, E., Gonzalez, A., Sauter, N. K., Phizackerley, R. P., Soltis, S. M., Kuhn, P. Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. (2002) J. Synchrotron Rad. 9, 401-406.

Data Monitoring with AI: Mendez, D., Holton, J. M., Lyubimov, A. Y., Hollatz, S., Mathews, I. I., Cichosz, A., Martirosyan, V., Zeng, T., Stofer, R., Liu, R., Song, J., McPhillips, S., Soltis, M. & Cohen, A. E. (2024). Deep residual networks for crystallography trained on synthetic data. Acta Cryst. D80, 26-43.

IOTA: Lyubimov, A.Y., Uervirojnangkoorn, M., Zeldin, O.B., Brewster, A.S., Murray, T.D., Sauter, N.K., Berger, J.M., Weis, W.I., Brunger, A.T. IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. J Appl Crystallogr. 2016 May 11;49 (pt 3):1057-1064.

Remote access: Soltis, S. M., Cohen, A. E., Deacon, A., Eriksson, T., Gonzalez, A., McPhillips, S., Chui, H. J., Dunten, P., Hollenbeck, M., Mathews, I. I., Miller, M., Moorhead, P., Phizackerley, R. P., Smith, C., Song, J., van dem Bedem, H., Ellis, P., Kuhn, P., McPhillips, T., Sauter, N., Sharp, K., Tsyba I. and Wolf G. New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection. (2008) Acta Cryst. D64, 1210-1221.

Stanford Automated Sample Exchange Robot (SAM)

• Cohen, A. E., Ellis, P. J., Miller, M. D., Deacon, A. M. and Phizackerley, R. P. An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot. (2002) J. Appl. Cryst. 35, 720-726.
• Russi, S., Song, J., McPhillips, S.E., and Cohen, A.E. The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines. (2016) J. Appl. Cryst. 49, 622.

UV/visible single-crystal microspectrophotometer at BL9-2: Cohen, A.E., Doukov, T., Soltis, M.S. UV-Visible Absorption Spectroscopy Enhanced X-ray Crystallography at Synchrotron and X-ray Free Electron Laser Sources. Protein Pept Lett. 2016;23(3):283-90.

Goniometer-based Serial Crystallography at SSRL and MFX: Cohen, A.E., Soltis, S.M., González, A., Aguila, L., Alonso-Mori, R., Barnes, C.O., Baxter, E.L., Brehmer, W., Brewster, A.S., Brunger, A.T., Calero, G., Chang, J.F., Chollet, M., Ehrensberger, P., Eriksson, T.L., Feng, Y., Hattne, J., Hedman, B., Hollenbeck, M., Holton, J.M., Keable, S., Kobilka, B.K., Kovaleva, E.G., Kruse, A.C., Lemke, H.T., Lin, G., Lyubimov, A.Y., Manglik, A., Mathews, I.I., McPhillips, S.E., Nelson, S., Peters, J.W., Sauter, N.K., Smith, C.A., Song, J., Stevenson, H.P., Tsai, Y., Uervirojnangkoorn, M., Vinetsky, V., Wakatsuki, S., Weis, W.I., Zadvornyy, O.A., Zeldin, O.B., Zhu, D., Hodgson, K.O. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A. 2014 Dec 2; 111(48):17122-7.

Derivative preparation with SSRL Xe-Kr cell: Cohen, A., Ellis, P., Kresge, N. & Soltis, S. M. MAD phasing with krypton. (2001) Acta Cryst. D57, 233-238.