2014 Tutorials

Welcome

Four example datasets from the LCLS are described here, with complete instructions for full data processing.

Getting Started

Go here to set up your environment.

List of Examples

Dataset	File Paths	Reference & purpose	CXIDB
L220 Lysozyme	/reg/d/psdm/cxi/cxi84914/xtc/e60	Boutet, 2012 (initial report) Hattne, 2014 (cctbx reprocessing)	17
Gd-Lysozyme	/reg/d/psdm/cxi/cxi84914/xtc/e239 /reg/d/psdm/cxi/cxi84914/xtc/e240	Barends, 2013 (SAD anomalous phasing)	22
L498 Thermolysin	/reg/d/psdm/cxi/cxi84914/xtc/e157	Hattne, 2014 (cctbx processing & weak Zn anomalous signal)	23
LB67 Thermolysin	/reg/d/psdm/cxi/cxi84914/xtc/e350	unpublished (illustrate CSPAD hi/lo gain settings)

References

• Hattne et al (2014): Accurate Macromolecular Structures Using Minimal Measurements from X-ray Free-electron Lasers. Nature Methods 11, 545-548. Reprint
• Brewster et al (2014): XFEL Detectors and ImageCIF. Computational Crystallography Newsletter 5, 19-24. Reprint
• Tran et al (2014): The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. Phil. Trans. R. Soc. B 369, 20130324. Reprint
• Kern et al (2014): Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers. Phil. Trans. R. Soc. B 369, 20130590. Reprint
• Parkhurst et al (2014): dxtbx: the diffraction experiment toolbox. J. Appl. Cryst. 47, 1459-1465. Reprint
• Kern et al (2014): Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications 5, 4371.
• Sawaya et al (2014): Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proc Natl Acad Sci USA, epub 18 Aug 2014.
• Waterman et al (2013): The DIALS framework for integration software. CCP4 Newsletter on Protein Crystallography 49, 16-19. Reprint
• Kern et al (2013) Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science 340, 491-495.
• Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N (2012) New Python-based methods for data processing. Acta Crystallographica Section D: Biological Crystallography D69, 1274-1282. Reprint
• Sierra et al (2012): Nanoflow electrospinning serial femtosecond crystallography. Acta Cryst. D68, 1584-1587. Reprint
• Kern et al (2012) Room temperature femtosecond X-ray diffraction of photosytem II microcrystals. Proc. Natl. Acad. Sci. USA 109, 9721-9726. Reprint