Towards phasing using high X-ray intensity

Analysis of serial femtosecond crystallography data collected at the Linac Coherent Light Source using two distinct photon fluxes shows different degrees of ionization of Gd atoms bound to a lysozyme protein, due to electronic damage processes. The charge contrast on the heavy atoms is quantified using difference Fourier maps, and the way in which this could be applied to phasing is discussed.

[1]  R. Santra,et al.  Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser , 2015 .

[2]  Anton Barty,et al.  Crystallographic data processing for free-electron laser sources , 2013, Acta crystallographica. Section D, Biological crystallography.

[3]  J. Hajdu,et al.  Potential for biomolecular imaging with femtosecond X-ray pulses , 2000, Nature.

[4]  Sébastien Boutet,et al.  De novo protein crystal structure determination from X-ray free-electron laser data , 2013, Nature.

[5]  M. Klintenberg,et al.  Radiation damage in biological material: Electronic properties and electron impact ionization in urea , 2008, 0808.1197.

[6]  Serge X. Cohen,et al.  Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 , 2008, Nature Protocols.

[7]  B. Krauskopf,et al.  Proc of SPIE , 2003 .

[8]  Stefan Zaefferer,et al.  New developments of computer-aided crystallographic analysis in transmission electron microscopy , 2000 .

[9]  Anton Barty,et al.  Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography , 2014, Nature Communications.

[10]  Georg Weidenspointner,et al.  Femtosecond X-ray protein nanocrystallography , 2011, Nature.

[11]  Carl Caleman,et al.  Diffraction before destruction , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[12]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[13]  Eric Girard,et al.  Gd-HPDO3A, a complex to obtain high-phasing-power heavy-atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozyme. , 2002, Acta crystallographica. Section D, Biological crystallography.

[14]  H. Chapman,et al.  Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[15]  Sébastien Boutet,et al.  The CSPAD megapixel x-ray camera at LCLS , 2012, Other Conferences.

[16]  Heike Soltau,et al.  Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. , 2013, Acta crystallographica. Section D, Biological crystallography.

[17]  S. T. Pratt,et al.  Femtosecond electronic response of atoms to ultra-intense X-rays , 2010, Nature.

[18]  Randy J. Read,et al.  Phenix - a comprehensive python-based system for macromolecular structure solution , 2012 .

[19]  S. French,et al.  On the treatment of negative intensity observations , 1978 .

[20]  Georg Weidenspointner,et al.  Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements , 2011, Nature Photonics.

[21]  Zbigniew Dauter,et al.  Biological Crystallography Structural Effects of Radiation Damage and Its Potential for Phasing , 2022 .

[22]  U Weierstall,et al.  Injector for scattering measurements on fully solvated biospecies. , 2012, The Review of scientific instruments.

[23]  Michael G. Rossmann,et al.  The single isomorphous replacement method , 1961 .

[24]  C. Bostedt,et al.  Femtosecond X-ray-induced explosion of C60 at extreme intensity , 2014, Nature Communications.

[25]  Anton Barty,et al.  Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data , 2014, Journal of applied crystallography.

[26]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[27]  G. Kartha,et al.  COMBINATION OF MULTIPLE ISOMORPHOUS REPLACEMENT AND ANOMALOUS DISPERSION DATA FOR PROTEIN STRUCTURE DETERMINATION. I. DETERMINATION OF HEAVY-ATOM POSITIONS IN PROTEIN DERIVATIVES. , 1965, Acta crystallographica.

[28]  S. Hau-Riege,et al.  Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulses. , 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

[29]  Anton Barty,et al.  Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser , 2013, Science.

[30]  D. S. Bradshaw,et al.  Photonics , 2023, 2023 International Conference on Electrical Engineering and Photonics (EExPolytech).

[31]  H. Chapman,et al.  Determination of multiwavelength anomalous diffraction coefficients at high x-ray intensity , 2013, 1305.3489.

[32]  Max H Nanao,et al.  Towards RIP using free-electron laser SFX data. , 2015, Journal of synchrotron radiation.

[33]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[34]  Sang-Kil Son,et al.  Multiwavelength anomalous diffraction at high x-ray intensity. , 2011, Physical review letters.

[35]  Anton Barty,et al.  CrystFEL: a software suite for snapshot serial crystallography , 2012 .

[36]  Anton Barty,et al.  Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser. , 2015, Optics express.

[37]  Sébastien Boutet,et al.  Room temperature femtosecond X-ray diffraction of photosystem II microcrystals , 2012, Proceedings of the National Academy of Sciences.

[38]  H. Chapman,et al.  Femtosecond protein nanocrystallography-data analysis methods. , 2010, Optics express.

[39]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[40]  A. Rudenko,et al.  Frustration of photoionization of Ar nanoplasma produced by extreme ultraviolet FEL pulses , 2013 .

[41]  Sébastien Boutet,et al.  Nanoflow electrospinning serial femtosecond crystallography. , 2012, Acta crystallographica. Section D, Biological crystallography.

[42]  Howard A. Scott,et al.  Cretin—a radiative transfer capability for laboratory plasmas , 2001 .

[43]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[44]  Sean McSweeney,et al.  Specific radiation damage can be used to solve macromolecular crystal structures. , 2003, Structure.

[45]  Carl Caleman,et al.  Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses , 2011 .

[46]  Kunio Hirata,et al.  Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses , 2014, Nature.

[47]  Georg Weidenspointner,et al.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. , 2011, Physical review. B, Condensed matter and materials physics.

[48]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[49]  Garth J. Williams,et al.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography , 2012, Science.

[50]  Sang-Kil Son,et al.  Impact of hollow-atom formation on coherent x-ray scattering at high intensity , 2011, 1101.4932.

[51]  Daniel Beisel,et al.  An anti-settling sample delivery instrument for serial femtosecond crystallography , 2012 .

[52]  Georg Weidenspointner,et al.  Ultra-efficient ionization of heavy atoms by intense X-ray free-electron laser pulses , 2012, Nature Photonics.

[53]  K. Schmidt,et al.  Gas dynamic virtual nozzle for generation of microscopic droplet streams , 2008, 0803.4181.