scholarly journals Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130333 ◽  
Author(s):  
Oleksandr Yefanov ◽  
Cornelius Gati ◽  
Gleb Bourenkov ◽  
Richard A. Kirian ◽  
Thomas A. White ◽  
...  

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure ‘three-dimensional merging’. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.

IUCrJ ◽  
2018 ◽  
Vol 5 (5) ◽  
pp. 574-584 ◽  
Author(s):  
Max O. Wiedorn ◽  
Salah Awel ◽  
Andrew J. Morgan ◽  
Kartik Ayyer ◽  
Yaroslav Gevorkov ◽  
...  

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s−1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.


2017 ◽  
Vol 50 (3) ◽  
pp. 830-839 ◽  
Author(s):  
S. M. Suturin ◽  
V. V. Fedorov ◽  
A. M. Korovin ◽  
N. S. Sokolov ◽  
A. V. Nashchekin ◽  
...  

The development of growth techniques aimed at the fabrication of nanoscale heterostructures with layers of ferroic 3dmetals on semiconductor substrates is very important for their potential usage in magnetic media recording applications. A structural study is presented of single-crystal nickel island ensembles grown epitaxially on top of CaF2/Si insulator-on-semiconductor heteroepitaxial substrates with (111), (110) and (001) fluorite surface orientations. The CaF2buffer layer in the studied multilayer system prevents the formation of nickel silicide, guides the nucleation of nickel islands and serves as an insulating layer in a potential tunneling spin injection device. The present study, employing both direct-space and reciprocal-space techniques, is a continuation of earlier research on ferromagnetic 3dtransition metals grown epitaxially on non-magnetic and magnetically ordered fluorides. It is demonstrated that arrays of stand-alone faceted nickel islands with a face-centered cubic lattice can be grown controllably on CaF2surfaces of (111), (110) and (001) orientations. The proposed two-stage nickel growth technique employs deposition of a thin seeding layer at low temperature followed by formation of the islands at high temperature. The application of an advanced three-dimensional mapping technique exploiting reflection high-energy electron diffraction (RHEED) has proved that the nickel islands tend to inherit the lattice orientation of the underlying fluorite layer, though they exhibit a certain amount of {111} twinning. As shown by scanning electron microscopy, grazing-incidence X-ray diffraction (GIXD) and grazing-incidence small-angle X-ray scattering (GISAXS), the islands are of similar shape, being faceted with {111} and {100} planes. The results obtained are compared with those from earlier studies of Co/CaF2epitaxial nanoparticles, with special attention paid to the peculiarities related to the differences in lattice structure of the deposited metals: the dual-phase hexagonal close-packed/face-centered cubic lattice structure of cobalt as opposed to the single-phase face-centered cubic lattice structure of nickel.


2018 ◽  
Vol 2 (4) ◽  
pp. 24 ◽  
Author(s):  
Anton Davydok ◽  
Thomas Cornelius ◽  
Zhe Ren ◽  
Cedric Leclere ◽  
Gilbert Chahine ◽  
...  

The three-point bending behavior of a single Au nanowire deformed by an atomic force microscope was monitored by coherent X-ray diffraction using a sub-micrometer sized hard X-ray beam. Three-dimensional reciprocal-space maps were recorded before and after deformation by standard rocking curves and were measured by scanning the energy of the incident X-ray beam during deformation at different loading stages. The mechanical behavior of the nanowire was visualized in reciprocal space and a complex deformation mechanism is described. In addition to the expected bending of the nanowire, torsion was detected. Bending and torsion angles were quantified from the high-resolution diffraction data.


2019 ◽  
Vol 26 (3) ◽  
pp. 660-676 ◽  
Author(s):  
Adrian P. Mancuso ◽  
Andrew Aquila ◽  
Lewis Batchelor ◽  
Richard J. Bean ◽  
Johan Bielecki ◽  
...  

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation – in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.


Author(s):  
David Blow

In Chapter 4 many two-dimensional examples were shown, in which a diffraction pattern represents the Fourier transform of the scattering object. When a diffracting object is three-dimensional, a new effect arises. In diffraction by a repetitive object, rays are scattered in many directions. Each unit of the lattice scatters, but a diffracted beam arises only if the scattered rays from each unit are all in phase. Otherwise the scattering from one unit is cancelled out by another. In two dimensions, there is always a direction where the scattered rays are in phase for any order of diffraction (just as shown for a one-dimensional scatterer in Fig. 4.1). In three dimensions, it is only possible for all the points of a lattice to scatter in phase if the crystal is correctly oriented in the incident beam. The amplitudes and phases of all the scattered beams from a three-dimensional crystal still provide the Fourier transform of the three-dimensional structure. But when a crystal is at a particular angular orientation to the X-ray beam, the scattering of a monochromatic beam provides only a tiny sample of the total Fourier transform of its structure. In the next section, we are going to find what is needed to allow a diffracted beam to be generated. We shall follow a treatment invented by Lawrence Bragg in 1913. Max von Laue, who discovered X-ray diffraction in 1912, used a different scheme of analysis; and Paul Ewald introduced a new way of looking at it in 1921. These three methods are referred to as the Laue equations, Bragg’s law and the Ewald construction, and they give identical results. All three are described in many crystallographic text books. Bragg’s method is straightforward, understandable, and suffices for present needs. I had heard J.J. Thomson lecture about…X-rays as very short pulses of radiation. I worked out that such pulses…should be reflected at any angle of incidence by the sheets of atoms in the crystal as if these sheets were mirrors.…It remained to explain why certain of the atomic mirrors in the zinc blende [ZnS] crystal reflected more powerfully than others.


2019 ◽  
Vol 88 (1) ◽  
pp. 35-58 ◽  
Author(s):  
Henry N. Chapman

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.


2014 ◽  
Vol 369 (1647) ◽  
pp. 20130337 ◽  
Author(s):  
Uwe Weierstall

X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques.


2008 ◽  
Vol 516 (22) ◽  
pp. 8022-8028 ◽  
Author(s):  
V. Holý ◽  
K. Mundboth ◽  
C. Mokuta ◽  
T.H. Metzger ◽  
J. Stangl ◽  
...  

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