Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

Reddy, Hemanth K. N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A.; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel S. D.; Loh, N. Duane; Maia, Filipe R. N. C.; Mancuso, Adrian P.; Muhlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C. H.; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu

doi:10.1038/sdata.2017.79

Title: Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

Abstract

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, the data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

Authors:

Reddy, Hemanth K. N. ^[1]; Yoon, Chun Hong ^[2]; Aquila, Andrew ^[2]; Awel, Salah ^[3];

^[4]; Barty, Anton ^[4];

^[5]; Bielecki, Johan ^[1]; Bobkov, Sergey ^[6]; Bucher, Maximilian ^[7]; Carini, Gabriella A. ^[2]; Carron, Sebastian ^[8];

^[3];

^[1];

^[2]; Ekeberg, Tomas ^[1]; Fromme, Petra ^[9]; Hajdu, Janos ^[10]; Hanke, Max Felix ^[1]; Hart, Philip ^[2] more »

Uppsala Univ., Uppsala (Sweden)
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
La Trobe Univ., Melbourne (Australia)
National Research Centre 'Kurchatov Institute', Moscow (Russia)
SLAC National Accelerator Lab., Menlo Park, CA (United States); Argonne National Lab. (ANL),Lemont, IL (United States); Technische Univ. Berlin, Berlin (Germany)
SLAC National Accelerator Lab., Menlo Park, CA (United States); California Lutheran Univ., Thousand Oaks, CA (United States)
Arizona State Univ., Tempe, AZ (United States)
Uppsala Univ., Uppsala (Sweden); Institute of Physics AS CR, Prague 8 (Czech Republic)
Univ. of Wisconsin, Milwaukee, WI (United States)
Univ. of Science and Technology, Pohang (Korea)
European X-ray Free Electron Laser GmbH, Schenefeld (Germany)
National Univ. of Singapore (Singapore)
Pohang Univ. of Science and Technology, Pohang (Korea)
Uppsala Univ., Uppsala (Sweden); AlbaNova Univ. Center, Stockholm (Sweden)
Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); National Research Nuclear Univ. MEPhI (Moscow Engineering Physics Institute), Moscow (Russia)
Brookhaven National Lab. (BNL), Upton, NY (United States)
Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany); Max-Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany)

Publication Date:: Tue Jun 27 00:00:00 EDT 2017

Research Org.:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1369312

Report Number(s):: SLAC-PUB-16952
Journal ID: ISSN 2052-4463; sdata201779

Grant/Contract Number:: AC02-76SF00515

Resource Type:: Accepted Manuscript

Journal Name:: Scientific Data

Additional Journal Information:: Journal Volume: 4; Journal ID: ISSN 2052-4463

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

Subject:: 46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY

Citation Formats


                    Reddy, Hemanth K. N., Yoon, Chun Hong, Aquila, Andrew, Awel, Salah, Ayyer, Kartik, Barty, Anton, Berntsen, Peter, Bielecki, Johan, Bobkov, Sergey, Bucher, Maximilian, Carini, Gabriella A., Carron, Sebastian, Chapman, Henry, Daurer, Benedikt, DeMirci, Hasan, Ekeberg, Tomas, Fromme, Petra, Hajdu, Janos, Hanke, Max Felix, Hart, Philip, Hogue, Brenda G., Hosseinizadeh, Ahmad, Kim, Yoonhee, Kirian, Richard A., Kurta, Ruslan P., Larsson, Daniel S. D., Loh, N. Duane, Maia, Filipe R. N. C., Mancuso, Adrian P., Muhlig, Kerstin, Munke, Anna, Nam, Daewoong, Nettelblad, Carl, Ourmazd, Abbas, Rose, Max, Schwander, Peter, Seibert, Marvin, Sellberg, Jonas A., Song, Changyong, Spence, John C. H., Svenda, Martin, Van der Schot, Gijs, Vartanyants, Ivan A., Williams, Garth J., and Xavier, P. Lourdu. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.  United States: N. p., 2017. 
Web.  doi:10.1038/sdata.2017.79.

Copy to clipboard


                    Reddy, Hemanth K. N., Yoon, Chun Hong, Aquila, Andrew, Awel, Salah, Ayyer, Kartik, Barty, Anton, Berntsen, Peter, Bielecki, Johan, Bobkov, Sergey, Bucher, Maximilian, Carini, Gabriella A., Carron, Sebastian, Chapman, Henry, Daurer, Benedikt, DeMirci, Hasan, Ekeberg, Tomas, Fromme, Petra, Hajdu, Janos, Hanke, Max Felix, Hart, Philip, Hogue, Brenda G., Hosseinizadeh, Ahmad, Kim, Yoonhee, Kirian, Richard A., Kurta, Ruslan P., Larsson, Daniel S. D., Loh, N. Duane, Maia, Filipe R. N. C., Mancuso, Adrian P., Muhlig, Kerstin, Munke, Anna, Nam, Daewoong, Nettelblad, Carl, Ourmazd, Abbas, Rose, Max, Schwander, Peter, Seibert, Marvin, Sellberg, Jonas A., Song, Changyong, Spence, John C. H., Svenda, Martin, Van der Schot, Gijs, Vartanyants, Ivan A., Williams, Garth J., & Xavier, P. Lourdu. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.  United States.  https://doi.org/10.1038/sdata.2017.79

Copy to clipboard


                    Reddy, Hemanth K. N., Yoon, Chun Hong, Aquila, Andrew, Awel, Salah, Ayyer, Kartik, Barty, Anton, Berntsen, Peter, Bielecki, Johan, Bobkov, Sergey, Bucher, Maximilian, Carini, Gabriella A., Carron, Sebastian, Chapman, Henry, Daurer, Benedikt, DeMirci, Hasan, Ekeberg, Tomas, Fromme, Petra, Hajdu, Janos, Hanke, Max Felix, Hart, Philip, Hogue, Brenda G., Hosseinizadeh, Ahmad, Kim, Yoonhee, Kirian, Richard A., Kurta, Ruslan P., Larsson, Daniel S. D., Loh, N. Duane, Maia, Filipe R. N. C., Mancuso, Adrian P., Muhlig, Kerstin, Munke, Anna, Nam, Daewoong, Nettelblad, Carl, Ourmazd, Abbas, Rose, Max, Schwander, Peter, Seibert, Marvin, Sellberg, Jonas A., Song, Changyong, Spence, John C. H., Svenda, Martin, Van der Schot, Gijs, Vartanyants, Ivan A., Williams, Garth J., and Xavier, P. Lourdu. Tue .  
"Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source".  United States.  https://doi.org/10.1038/sdata.2017.79.  https://www.osti.gov/servlets/purl/1369312.

Copy to clipboard


                    
@article{osti_1369312,

  title        = {Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source},

  author       = {Reddy, Hemanth K. N. and Yoon, Chun Hong and Aquila, Andrew and Awel, Salah and Ayyer, Kartik and Barty, Anton and Berntsen, Peter and Bielecki, Johan and Bobkov, Sergey and Bucher, Maximilian and Carini, Gabriella A. and Carron, Sebastian and Chapman, Henry and Daurer, Benedikt and DeMirci, Hasan and Ekeberg, Tomas and Fromme, Petra and Hajdu, Janos and Hanke, Max Felix and Hart, Philip and Hogue, Brenda G. and Hosseinizadeh, Ahmad and Kim, Yoonhee and Kirian, Richard A. and Kurta, Ruslan P. and Larsson, Daniel S. D. and Loh, N. Duane and Maia, Filipe R. N. C. and Mancuso, Adrian P. and Muhlig, Kerstin and Munke, Anna and Nam, Daewoong and Nettelblad, Carl and Ourmazd, Abbas and Rose, Max and Schwander, Peter and Seibert, Marvin and Sellberg, Jonas A. and Song, Changyong and Spence, John C. H. and Svenda, Martin and Van der Schot, Gijs and Vartanyants, Ivan A. and Williams, Garth J. and Xavier, P. Lourdu},

  abstractNote = {Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, the data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.},

  doi          = {10.1038/sdata.2017.79},

  journal      = {Scientific Data},

  number       = ,

  volume       = 4,

  place        = {United States},

  year         = {Tue Jun 27 00:00:00 EDT 2017},

  month        = {Tue Jun 27 00:00:00 EDT 2017}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

https://doi.org/10.1038/sdata.2017.79

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 36 works

Citation information provided by
Web of Science

Figures / Tables:

Figure 1: Electron micrograph of purified bacteriophage PR772. Scale bar represents 100 nm.

All figures and tables (5 total)

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Single mimivirus particles intercepted and imaged with an X-ray laser
journal, February 2011

Seibert, M. Marvin; Ekeberg, Tomas; Maia, Filipe R. N. C.
Nature, Vol. 470, Issue 7332
DOI: 10.1038/nature09748

The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source
journal, April 2015

Ferguson, Ken R.; Bucher, Maximilian; Bozek, John D.
Journal of Synchrotron Radiation, Vol. 22, Issue 3
DOI: 10.1107/S1600577515004646

High-throughput imaging of heterogeneous cell organelles with an X-ray laser
journal, November 2014

Hantke, Max F.; Hasse, Dirk; Maia, Filipe R. N. C.
Nature Photonics, Vol. 8, Issue 12
DOI: 10.1038/nphoton.2014.270

Hummingbird : monitoring and analyzing flash X-ray imaging experiments in real time
journal, April 2016

Daurer, Benedikt J.; Hantke, Max F.; Nettelblad, Carl
Journal of Applied Crystallography, Vol. 49, Issue 3
DOI: 10.1107/S1600576716005926

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
journal, August 2016

Munke, Anna; Andreasson, Jakob; Aquila, Andrew
Scientific Data, Vol. 3, Issue 1
DOI: 10.1038/sdata.2016.64

Single Particle X-ray Diffractive Imaging
journal, January 2008

Bogan, Michael J.; Benner, W. Henry; Boutet, Sébastien
Nano Letters, Vol. 8, Issue 1, p. 310-316
DOI: 10.1021/nl072728k

First lasing and operation of an ångstrom-wavelength free-electron laser
journal, August 2010

Emma, P.; Akre, R.; Arthur, J.
Nature Photonics, Vol. 4, Issue 9
DOI: 10.1038/nphoton.2010.176

Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges
journal, July 2015

Hosseinizadeh, A.; Dashti, A.; Schwander, P.
Structural Dynamics, Vol. 2, Issue 4
DOI: 10.1063/1.4919740

Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser
journal, March 2015

Ekeberg, Tomas; Svenda, Martin; Abergel, Chantal
Physical Review Letters, Vol. 114, Issue 9
DOI: 10.1103/PhysRevLett.114.098102

Potential for biomolecular imaging with femtosecond X-ray pulses
journal, August 2000

Neutze, Richard; Wouts, Remco; van der Spoel, David
Nature, Vol. 406, Issue 6797
DOI: 10.1038/35021099

The linac coherent light source single particle imaging road map
journal, July 2015

Aquila, A.; Barty, A.; Bostedt, C.
Structural Dynamics, Vol. 2, Issue 4
DOI: 10.1063/1.4918726

The Coherent X-ray Imaging Data Bank
journal, August 2012

Maia, Filipe R. N. C.
Nature Methods, Vol. 9, Issue 9
DOI: 10.1038/nmeth.2110

Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers
journal, October 2015

Bobkov, S. A.; Teslyuk, A. B.; Kurta, R. P.
Journal of Synchrotron Radiation, Vol. 22, Issue 6
DOI: 10.1107/S1600577515017348

Linac Coherent Light Source data analysis using psana
journal, March 2016

Damiani, D.; Dubrovin, M.; Gaponenko, I.
Journal of Applied Crystallography, Vol. 49, Issue 2
DOI: 10.1107/S1600576716004349

Gas dynamic virtual nozzle for generation of microscopic droplet streams
journal, September 2008

DePonte, D. P.; Weierstall, U.; Schmidt, K.
Journal of Physics D: Applied Physics, Vol. 41, Issue 19, Article No. 195505
DOI: 10.1088/0022-3727/41/19/195505

Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources
journal, March 2010

Strüder, Lothar; Epp, Sascha; Rolles, Daniel
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 614, Issue 3
DOI: 10.1016/j.nima.2009.12.053

Effects of extraneous noise in cryptotomography
conference, October 2012

Loh, N. Duane
SPIE Optical Engineering + Applications, SPIE Proceedings
DOI: 10.1117/12.930165

Novel algorithms in coherent diffraction imaging using x-ray free-electron lasers
conference, October 2012

Yoon, Chunhong
SPIE Optical Engineering + Applications, SPIE Proceedings
DOI: 10.1117/12.953634