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, G.; Carron, S.; Chapman, Henry N.; Daurer, Benedikt J.; DeMi̇rci̇, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, János; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel; Loh, N. Duane; Maia, Filipe R. N. C.; Mancuso, Adrian P.; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, A.; Rose, M. Franklin; Schwander, Peter; Seibert, M. Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C. H.; Svenda, Martin; Schot, Gijs van der; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu

doi:10.1038/sdata.2017.79

Cited by 59 publications

(54 citation statements)

References 21 publications

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“…A detailed description of the experimental setup and sample preparation can be found in Ref. [67]. A large scattering data set containing about 3 × 10 6 diffraction patterns was filtered to select only high-intensity single hits with more than 4500 ADUs/pixel on average.…”

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confidence: 99%

“…These patterns were further classified according to the scattering particle size to minimize polydispersity effects (see Refs. [57,67] for preprocessing details). The resulting data sets with polydispersity PD = 3 nm used in the following analysis contained 332 diffraction patterns from rice dwarf virus (RDV) particles, with size variation from 69 to 72 nm, and 566 patterns from PR772 bacteriophage particles, with size variation from 67.5 to 70.5 nm.…”

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confidence: 99%

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Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

et al. 2017

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We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

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confidence: 99%

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Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

et al. 2017

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“…SPI benefits from the superbright X-ray pulses generated by an XFEL, and SPI technology can image nanoscale samples effectively without the need for crystallization [90]. As a successful technique for SPI research, aerosol injector has been successfully used in the study of viruses [86][87][88]91], soot [92], cells [93], cell components [94], and so on.…”

Section: Aerosol Injectormentioning

confidence: 99%

A guide to sample delivery systems for serial crystallography

et al. 2019

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Crystallography has made a notable contribution to our knowledge of structural biology. For traditional crystallography experiments, the growth of crystals with large size and high quality is crucial, and it remains one of the bottlenecks. In recent years, the successful application of serial femtosecond crystallography (SFX) provides a new choice when only numerous microcrystals can be obtained. The intense pulsed radiation of X‐ray free‐electron lasers (XFELs) enables the data collection of small‐sized crystals, making the size of crystals no longer a limiting factor. The ultrafast pulses of XFELs can achieve ‘diffraction before destruction’, which effectively avoids radiation damage and realizes diffraction near physiological temperatures. More recently, the SFX has been expanded to serial crystallography (SX) that can additionally employ synchrotron radiation as the light source. In addition to the traditional ones, these techniques provide complementary opportunities for structural determination. The development of SX experiments strongly relies on the advancement of hardware including the sample delivery system, the X‐ray source, and the X‐ray detector. Here, in this review, we categorize the existing sample delivery systems, summarize their progress, and propose their future prospectives.

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“…(a) Single-particle hit; (b) multiple-particle hit; (c) water diffraction that may contain contaminant residue from samples and buffer solutions; (d) background diffraction from detector; (e) detector defect pattern. (reproduced with permission from [197]. Copyright Springer Nature, 2017).…”

Section: Summary and Future Prospectsmentioning

confidence: 99%

“…Diffusion map algorithms provide mathematical links to a cloud of points via the Laplace-Beltrami operator. Each point on a diffusion map represents a diffraction pattern as shown on Figure 9 [197]. Single hit, multiple-particle hit, water diffraction, background and defects from the detector are captured in such mapping.…”

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Current Status of Single Particle Imaging with X-ray Lasers

Sun

Fan

et al. 2018

Applied Sciences

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Abstract:The advent of ultrafast X-ray free-electron lasers (XFELs) opens the tantalizing possibility of the atomic-resolution imaging of reproducible objects such as viruses, nanoparticles, single molecules, clusters, and perhaps biological cells, achieving a resolution for single particle imaging better than a few tens of nanometers. Improving upon this is a significant challenge which has been the focus of a global single particle imaging (SPI) initiative launched in December 2014 at the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, USA. A roadmap was outlined, and significant multi-disciplinary effort has since been devoted to work on the technical challenges of SPI such as radiation damage, beam characterization, beamline instrumentation and optics, sample preparation and delivery and algorithm development at multiple institutions involved in the SPI initiative. Currently, the SPI initiative has achieved 3D imaging of rice dwarf virus (RDV) and coliphage PR772 viruses at~10 nm resolution by using soft X-ray FEL pulses at the Atomic Molecular and Optical (AMO) instrument of LCLS. Meanwhile, diffraction patterns with signal above noise up to the corner of the detector with a resolution of~6 Ångström (Å) were also recorded with hard X-rays at the Coherent X-ray Imaging (CXI) instrument, also at LCLS. Achieving atomic resolution is truly a grand challenge and there is still a long way to go in light of recent developments in electron microscopy. However, the potential for studying dynamics at physiological conditions and capturing ultrafast biological, chemical and physical processes represents a tremendous potential application, attracting continued interest in pursuing further method development. In this paper, we give a brief introduction of SPI developments and look ahead to further method development.

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

Cited by 59 publications

References 21 publications

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

A guide to sample delivery systems for serial crystallography

Current Status of Single Particle Imaging with X-ray Lasers

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