Macromolecular Imaging using X-ray free-electron lasers*
01 Jun 2018-Vol. 64, Iss: 1, pp 415-435
TL;DR: New techniques for determining the structure of systems that cannot be crystallized and for studying the time-resolved behavior of irreversible reactions at femtosecond timescales are now available.
Abstract: X-ray crystallography, which is used for the determination of most biomolecular structures, has relied on Bragg diffraction from single crystals for more than a century. For many difficult to crystallize proteins, the growth of large well-ordered single crystals is a major challenge. Single molecule diffraction is a challenging but highly desired approach to structure determination, as it abolishes the need for crystallization and provides about four times higher information content than needed to solve a structure, unlike Bragg diffraction which is usually insufficient for direct phasing. Even using the powerful X-ray Free Electron Lasers, the challenges of this method have so far not been overcome to acquire atomic resolution structures. Recently, it was shown that the structure of a protein can be solved based on continuous diffraction from crystals with translational disorder.
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TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.
Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
6,313 citations
University of Hamburg1, Max Planck Society2, Fundamental Research on Matter Institute for Atomic and Molecular Physics3, Kansas State University4, Lund University5, Technical University of Berlin6, SLAC National Accelerator Laboratory7, Uppsala University8, Aarhus University9, Arizona State University10, University of Siegen11
TL;DR: In this paper, the authors reported experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source.
Abstract: We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, eg, structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules
229 citations
Cites background from "Macromolecular Imaging using X-ray ..."
...The forthcoming European XFEL facility will give the opportunity to collect patterns at a rate of 27 000 per second, which could be sufficient to collect the necessary 105–108 patterns within minutes or hours [13]....
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...However, the path to actual determination of atomically resolved structures and dynamics of single molecules is still long [13]....
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...Nevertheless, related experiments on the investigation of small-molecule structures and their dynamics utilizing molecular ensembles are within reach [13, 17]....
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...molecular processes under well-defined conditions it was proposed [13, 17] to spatially separate shapes [18], sizes [19], or individual isomers [20–22] of complex small molecules before delivery to the interaction point of an XFEL....
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...[13] Anton Barty, Jochen Küpper, and Henry N Chapman, “Molecular imaging using x-ray free-electron lasers,” Annu....
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TL;DR: The room-temperature structure of lysozyme is determined using 40000 individual diffraction patterns from micro-crystals flowing in liquid suspension across a synchrotron microfocus beamline.
200 citations
TL;DR: In this paper, the authors discuss recent experimental and theoretical developments in ultrafast X-ray absorption spectroscopies (XAS) and explore the new opportunities they offer, as well as the driving force for new theoretical methods permitting a detailed interpretation of the spectra in terms of the geometrical and electronic properties of the system.
181 citations
TL;DR: A relaxation of averaged alternating reflectors and determine the fixed-point set of the related operator in the convex case is proposed and the effectiveness of the algorithm compared to the current state of the art is demonstrated.
Abstract: We report on progress in algorithms for iterative phase retrieval. The theory of convex optimization is used to develop and to gain insight into counterparts for the nonconvex problem of phase retrieval. We propose a relaxation of averaged alternating reflectors and determine the fixed point set of the related operator in the convex case. A numerical study supports our theoretical observations and demonstrates the effectiveness of the algorithm compared to the current state of the art.
174 citations
References
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49,597 citations
Journal Article•
TL;DR: In this article, an algorithm is presented for the rapid solution of the phase of the complete wave function whose intensity in the diffraction and imaging planes of an imaging system are known.
5,197 citations
"Macromolecular Imaging using X-ray ..." refers background in this paper
...Computational techniques for phasing optical diffraction patterns were first proposed by Gerchberg & Saxton (20) and later refined by Fienup (21), with their origins going back to an early paper by Sayre (22)....
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...Gerchberg RW, Saxton WO....
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TL;DR: The Linac Coherent Light Source free-electron laser has achieved coherent X-ray generation down to a wavelength of 1.2 A and at a brightness that is nearly ten orders of magnitude higher than conventional synchrotrons.
Abstract: The Linac Coherent Light Source free-electron laser has now achieved coherent X-ray generation down to a wavelength of 1.2 A and at a brightness that is nearly ten orders of magnitude higher than conventional synchrotrons. Researchers detail the first operation and beam characteristics of the system, which give hope for imaging at atomic spatial and temporal scales.
2,648 citations
TL;DR: Novel features are a suite of operations relating to the determination, modeling, and correction of the contrast transfer function and the availability of the entire documentation in hypertext format.
2,117 citations
TL;DR: Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens was proposed in this paper, where the authors extended the methodology to allow the imaging of micro-scale specimens.
Abstract: Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens
1,791 citations