2014 Tutorials

Welcome

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

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LB67 Thermolysin	/reg/d/psdm/cxi/cxi84914/xtc/e350	unpublished (illustrate CSPAD hi/lo gain settings)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 AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK (2014): XFEL Detectors and ImageCIF. <a href="http://www.phenix-online.org/newsletter"> Computational Crystallography Newsletter 5, 19-24</a>. <a href="http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf" target=reprints >(Reprint)</a>
• Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, Yachandra V (2014): The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. <a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130324.full.pdf+html"> Phil. Trans. R. Soc. B 369, 20130324. </a> <a href="http://dx.doi.org/10.1098/rstb.2013.0324" target=reprints >(Reprint)</a>
• Kern J, Hattne J, Tran R, Alonso-Mori R, Laksmono H, Gul S, Sierra RG, Rehanek J, Erko A, Mitzner R, Wernet P, Bergman n U, Sauter NK, Yachandra V, Yano J (2014): Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers. <a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html"> Phil. Trans. R. Soc. B 369, 20130590. </a> <a href="http://dx.doi.org/10.1098/rstb.2013.0590" target=reprints >(Reprint)</a>
• Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton, AW, Echols N, Evans G, Sauter NK, Winter G (2014): dxtbx: the diffraction experiment toolbox. <a href="http://dx.doi.org/10.1107/S1600576714011996"> J. Appl. Cryst. 47, 1459-1465. <a href="http://cci.lbl.gov/publications/download/jo5001_reprint.pdf" target=reprints >(Reprint)</a>
• Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE , Gallo E, Uhlig J, Sokaras D, Weng T-C, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sau ter NK, Bergmann U, Yano J, Yachandra VK (2014): Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. <a href="http://dx.doi.org/10.1038/ncomms5371"> Nature Communications 5, 4371</a>. <a target=reprints >(Reprint)</a>

• Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier J-P, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park H-W, Federici BA, Sauter NK, Schlichting I, Eisenberg DS (2014): Protein crystal structure obtained at 2.9 &Aring resolution from injecting bacterial cells into an X-ray free-electron laser beam. <a href="http://www.pnas.org/content/early/2014/08/14/1413456111"> Proc Natl Acad Sci USA, epub 18 Aug 2014</a>. <a target=reprints >(Reprint)</a>
• Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J, Brewster A, Sauter NK, Evans G (2013): The DIALS framework for integration software. <a href="http://www.ccp4.ac.uk/newsletters/newsletter49/content.html"> CCP4 Newsletter on Protein Crystallography 49, 16-19</a>. <a href="http://cci.lbl.gov/publications/download/DIALS.pdf" target=reprints >(Reprint)</a>

• 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