scholarly journals Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction

2007 ◽  
Vol 64 (1) ◽  
pp. 33-35 ◽  
Author(s):  
D. Sayre
Keyword(s):  
Single Particle ◽  
High Vacuum ◽  
Three Dimensional ◽  
X Rays ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
Three Dimensional Imaging ◽  
X Ray ◽  
X Ray Crystallography ◽  
A Cell

Single-particle X-ray diffraction is an extension of X-ray crystallography which allows the specimen to be any small solid-state bounded object; in Shapiroet al.[Proc. Natl Acad. Sci. USA(2005),102, 15343–15346] and Thibaultet al.[Acta Cryst.(2006), A62, 248–261], the reader can find descriptions of a recent StonyBrook/Berkeley/Cornell two-dimensional imaging of a yeast cell by this technique. Our present work is aimed at extending the technique to the three-dimensional imaging of a cell. However, the usual method of doing that, namely rotating the specimen into many orientations in the X-ray beam, has not as yet given sufficiently good three-dimensional diffraction data to allow the work to go forward, the largest problem being the difficulty of preventing unwanted levels of change in the specimen through the extended exposure to a hostile environment of X-rays and, in some cases, high vacuum and/or extreme cold. The present paper discusses possible methods of dealing with this problem.

scholarly journals Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction. Addendum

2007 ◽  
Vol 64 (1) ◽  
pp. 36-37 ◽  
Author(s):  
David A. Shapiro
Keyword(s):  
Three Dimensional ◽  
Biological Cell ◽  
X Ray Diffraction ◽  
Short Term ◽  
Acta Cryst ◽  
Three Dimensional Imaging ◽  
X Ray ◽  
Structural Problems ◽  
Material Sciences ◽  
Diffraction Microscopy

In the paper by Sayre [Acta Cryst.(2008), A64, 33–35], a proposal is made to use stereoscopy as a short-term means of overcoming the primarily technological hurdles involved in three-dimensional imaging of the biological cell by soft X-ray diffraction microscopy. This addendum provides a broader perspective on the techniques used by this rapidly maturing community to investigate structural problems in the biological and material sciences.

Recent Developments In Monochromatic Microprobe X-Ray Fluorescence (MMXRF)

1998 ◽  
Vol 4 (S2) ◽  
pp. 378-379
Author(s):  
Z. W. Chen ◽  
D. B. Wittry
Keyword(s):  
Materials Science ◽  
High Vacuum ◽  
Three Dimensional ◽  
High Sensitivity ◽  
X Rays ◽  
Fluorescence Excitation ◽  
X Ray ◽  
Quantitative Microanalysis ◽  
Recent Developments ◽  
Fifth Order

A monochromatic x-ray microprobe based on a laboratory source has recently been developed in our laboratory and used for fluorescence excitation. This technique provides high sensitivity (ppm to ppb), nondestructive, quantitative microanalysis with minimum sample preparation and does not require a high vacuum specimen chamber. It is expected that this technique (MMXRF) will have important applications in materials science, geological sciences and biological science.Three-dimensional focusing of x-rays can be obtained by using diffraction from doubly curved crystals. In our MMXRF setup, a small x-ray source was produced by the bombardment of a selected target with a focused electron beam and a toroidal mica diffractor with Johann pointfocusing geometry was used to focus characteristic x-rays from the source. In the previous work ∼ 108 photons/s were obtained in a Cu Kα probe of 75 μm × 43 μm in the specimen plane using the fifth order reflection of the (002) planes of mica.

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

scholarly journals Three-dimensional Imaging of Nanoscale Internal Structure by Coherent X-ray Diffraction Microscope

Materia Japan ◽  
2007 ◽  
Vol 46 (12) ◽  
pp. 827-827
Author(s):  
Yoshinori Nishino ◽  
Yukio Takahashi ◽  
Tetsuya Ishikawa ◽  
Eiichiro Matsubara
Keyword(s):  
Internal Structure ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Three Dimensional Imaging ◽  
X Ray

scholarly journals Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography

2019 ◽  
Vol 377 (2145) ◽  
pp. 20170474 ◽  
Author(s):  
Christopher D. M. Hutchison ◽  
Jasper J. van Thor
Keyword(s):  
Structural Dynamics ◽  
Time Domain ◽  
Optical Pumping ◽  
High Repetition Rate ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Vibrational Coherence ◽  
X Ray Crystallography ◽  
Ultrafast Optical

Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.

Three-dimensional imaging of dislocations by X-ray diffraction laminography

2012 ◽  
Vol 101 (24) ◽  
pp. 244103 ◽  
Author(s):  
D. Hänschke ◽  
L. Helfen ◽  
V. Altapova ◽  
A. Danilewsky ◽  
T. Baumbach
Keyword(s):  
Three Dimensional ◽  
X Ray Diffraction ◽  
Three Dimensional Imaging ◽  
X Ray

scholarly journals The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 580
Author(s):  
Victor R.A. Dubach ◽  
Albert Guskov
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Fourier Transform

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.

scholarly journals William Lawrence Bragg, 31 March 1890 - 1 July 1971

1979 ◽  
Vol 25 ◽  
pp. 74-143 ◽  
Keyword(s):  
Living Cell ◽  
Inorganic Compounds ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Intensive Work ◽  
Unique Part

Walking along the Backs in Cambridge one day in the autumn of 1912 William Lawrence Bragg had an idea that led immediately to a dramatic advance in physics and has since transformed chemistry, mineralogy, metallurgy and, most recently, biology. He realized that the observations of X-ray diffraction by a crystal, which had been reported by von Laue and his associates earlier in that year, can be interpreted very simply as arising from reflexion of the X-rays by planes of atoms in the crystal and hence that the X-ray observations provide evidence from which the arrangement of atoms in the crystal may be determined. A few weeks of intensive work on simple inorganic compounds were enough to demonstrate the correctness of these ideas but the development of the method, at first in association with his father and later as the leader or guiding influence of a host of workers, was the labour of a lifetime. When he died on 1 July 1971, X-ray crystallography had revealed the arrangement of atoms in matter of all kinds from the simplest of salts to the macromolecules of the living cell. The story of his life is very largely the story of that achievement and the circumstances that led to his unique part in it.

Three-Dimensional Coherent X-Ray Diffraction Microscopy

MRS Bulletin ◽  
2004 ◽  
Vol 29 (3) ◽  
pp. 177-181 ◽  
Author(s):  
Ian K. Robinson ◽  
Jianwei Miao
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Real Space ◽  
Objective Lens ◽  
X Rays ◽  
X Ray Diffraction ◽  
Space Images ◽  
Thin Sections ◽  
X Ray ◽  
Penetration Ability

AbstractX-rays have been widely used in the structural analysis of materials because of their significant penetration ability, at least on the length scale of the granularity of most materials. This allows, in principle, for fully three-dimensional characterization of the bulk properties of a material. One of the main advantages of x-ray diffraction over electron microscopy is that destructive sample preparation to create thin sections is often avoidable. A major disadvantage of x-ray diffraction with respect to electron microscopy is its inability to produce real-space images of the materials under investigation—there are simply no suitable lenses available. There has been significant progress in x-ray microscopy associated with the development of lenses, usually based on zone plates, Kirkpatrick–Baez mirrors, or compound refractive lenses. These technologies are far behind the development of electron optics, particularly for the large magnification ratios needed to attain high resolution. In this article, the authors report progress toward the development of an alternative general approach to imaging, the direct inversion of diffraction patterns by computation methods. By avoiding the use of an objective lens altogether, the technique is free from aberrations that limit the resolution, and it can be highly efficient with respect to radiation damage of the samples. It can take full advantage of the three-dimensional capability that comes from the x-ray penetration. The inversion step employs computational methods based on oversampling to obtain a general solution of the diffraction phase problem.

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