Frontier methods in coherent X-ray diffraction for high-resolution structure determination

2016 ◽  
Vol 49 ◽  
Author(s):  
Marcus Gallagher-Jones ◽  
Jose A. Rodriguez ◽  
Jianwei Miao
Keyword(s):  
Structure Determination ◽  
X Rays ◽  
X Ray Diffraction ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
X Ray Crystallography ◽  
Max Von Laue ◽  
Complex Protein ◽  
High Resolution Structure

AbstractIn 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.

scholarly journals Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

2016 ◽  
Vol 23 (5) ◽  
pp. 1210-1215 ◽  
Author(s):  
Jonathan Logan ◽  
Ross Harder ◽  
Luxi Li ◽  
Daniel Haskel ◽  
Pice Chen ◽  
...  
Keyword(s):  
Magnetic Circular Dichroism ◽  
Three Dimensional ◽  
Control Sample ◽  
Magnetic Ordering ◽  
X Rays ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
Diffraction Patterns ◽  
A New Technique

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. The performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd5Si2Ge2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. These tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd5Si2Ge2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.

The Evolution of X-Ray Instrumentation at Rich. Seifert & Co.

1995 ◽  
Vol 39 ◽  
pp. 47-56
Author(s):  
A. Haase
Keyword(s):  
World War Ii ◽  
World War I ◽  
Science And Technology ◽  
German Language ◽  
X Rays ◽  
X Ray Diffraction ◽  
World War ◽  
Executive Management ◽  
X Ray ◽  
Max Von Laue

To facilitate orientation in time, some selected events will be briefly presented. Approximately five hundred years ago, Columbus discovered America. One hundred years ago, on November 8th, 1895, Wilhelm Conrad R6ntgen discovered the X-rays which in the German language are called after him. In 1912 Max von Laue conducted the first X-ray diffraction experiment. In 1892 Richard Seifert Sr. founded the Electrotechnical Plant in Hamburg. After World War I (1914-1918) the company founder gradually handed the firm over to his son Richard Seifert Jr. After his son had completed studies in physics and electrical engineering he conducted pioneering experiments on the application of X-rays in science and technology. From the very beginning, X-ray equipment was produced in the three fields of medicine, science and technology. It was only ten years after World War II (1939-1945) that the line of medical equipment was discontinued and the daughter [1] as a member of the third generation gradually took over executive management tasks.

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’.

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.

X-ray analysis

1999 ◽  
Author(s):  
L. Sawyer ◽  
M. A. Turner
Keyword(s):  
Structure Determination ◽  
Protein Crystallography ◽  
General Description ◽  
X Rays ◽  
Actual Structure ◽  
X Ray ◽  
Preliminary Characterization ◽  
X Ray Crystallography ◽  
Full Structure ◽  
Unit Cell Dimensions

This chapter covers the preliminary characterization of the crystals in order to determine if they are suitable for a full structure determination. Probably more frustrating than failure to produce crystals at all, is the growth of beautiful crystals which do not diffract, which have very large unit cell dimensions, or which decay very rapidly in the X-ray beam, though this last problem has been largely overcome by freezing the sample. It is impossible in one brief chapter to give more than a flavour of what the X-ray crystallographic technique entails and it is assumed that the protein chemist growing the crystals will have contact with a protein crystallographer, who will carry out the actual structure determination and in whose laboratory state-of-the-art facilities exist. However, preliminary characterization can often be carried out with little more than the equipment which is widely available in Chemistry and Physics Departments and so the crystal grower remote from a protein crystallography laboratory can monitor the success of their experiments. The reader should refer to the first edition for protocols useful for photographic characterization but such techniques are seldom used nowadays. It must be remembered, in any case, that X-rays are dangerous and the inexperienced should not try to X-ray protein crystals without help. It is necessary to provide an overview of X-ray crystallography, to put the preliminary characterization in context. For a general description of the technique the reader should refer to Glusker et al. (1) or Stout and Jensen (2). For protein crystallography in particular, the books by McRee (3) and Drenth (4) describe many of the advances since the seminal work of Blundell and Johnson (5). Amongst many excellent introductory articles, those by Bragg (6), published years ago, and Glusker (7) are particularly recommended. The scattering or diffraction of X-rays is an interference phenomenon and the interference between the X-rays scattered from the atoms in the structure produces significant changes in the observed diffraction in different directions. This variation in intensity with direction arises because the path differences taken by the scattered X-ray beams are of the same magnitude as the separation of the atoms in the molecule.

Outline of Crystallography for Biologists

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Biological Sciences ◽  
Structure Determination ◽  
Mathematical Knowledge ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Critical Insight ◽  
Insight Into ◽  
Extensive Reference ◽  
Reference Section

Outline of Crystallography for Biologists is intended for researchers and students in the biological sciences who require an insight into the methods of X-ray crystallography without needing to learn all the relevant theory. The main text is purely descriptive and is readable by those with minimal mathematical knowledge. Some mathematical detail is given throughout in boxes, but these can be ignored. Theory is limited to the essentials required to comprehend issues of quality. There is an extensive reference section and suggestions for further reading for those who wish to delve deeper. The first part 'Fundamentals' presents the underlying ideas which allow x-ray structure analysis to be carried out and provides an appropriate background to courses in structural determination. The second part 'Practice' gives more information about the procedures employed in the course of crystal structure determination. The emphasis is on the quality measures of X-ray diffraction analysis to give the reader a critical insight into the quality and accuracy of a structure determination and to enable the reader to appreciate which parts of a structure determination may have caused special difficulty. There is no pretence of completeness and many matters discussed in standard crystallography texts are deliberately omitted. However, issues not brought out in the standard texts are discussed, making it a useful resource for non-practising crystallographers as well.

scholarly journals Polarimetric coherent diffraction imaging on cancer-associated fibroblasts and SARS-CoV-2 viruses

2021 ◽  
Author(s):  
Xiaowen Shi ◽  
Dmitry Karpov ◽  
Zach Barringer ◽  
Elijah Schold ◽  
Demba Sarr ◽  
...  
Keyword(s):  
High Resolution ◽  
Imaging Techniques ◽  
Complex Refractive Index ◽  
Cancer Associated Fibroblasts ◽  
X Rays ◽  
Label Free ◽  
Diffractive Imaging ◽  
Dynamical Interaction ◽  
X Ray ◽  
Coherent Diffractive Imaging

Abstract Simultaneously non-destructive, high resolution, and label-free imaging are of paramount importance for studies of complex biological systems, from viruses to cell cultures. Electron imaging techniques achieve extreme resolution but require slicing the sample to obtain volumetric information. On the other hand, X-rays’ high penetrative ability combined with cryogenic temperatures allows access to high resolution while preserving the sample’s structure. However, both X-ray and electron techniques do not currently allow label-free imaging with tissue specificity. Here, we combine a polarimetric approach with coherent diffractive imaging to reveal new ways to overcome this by mapping variations of anisotropy in the complex refractive index of cellular structures to differentiate between various tissues without chemical labeling. In this article, we demonstrate imaging of cancer-associated fibroblasts using birefringent coherent diffractive imaging with enhanced sensitivity to fibrous structures and their orientation as well as the possibility to differentiate the nucleus of the cell. We also propose a modeled soft X-ray experiment on the SARS-CoV-2 virus to address the possibility of leveraging the polarimetric birefringent contrast to spatially resolve the dynamical interaction of the virus with its host environment. We hope that our approach can open up avenues in the future to map and understand how SARS viruses bind with human epithelial cells.

Introduction

2010 ◽  
Author(s):  
Jenny Pickworth Glusker ◽  
Kenneth N. Trueblood
Keyword(s):  
Diffraction Pattern ◽  
Three Dimensional ◽  
Spectroscopic Studies ◽  
Ring Structure ◽  
Chloride Ions ◽  
Experimental Result ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Max Von Laue

Much of our present knowledge of the architecture of molecules has been obtained from studies of the diffraction of X rays or neutrons by crystals. X rays are scattered by the electrons of atoms and ions, and the interference between the X rays scattered by the different atoms or ions. in a crystal can result in a diffraction pattern. Similarly, neutrons are scattered by the nuclei of atoms. Measurements on a crystal diffraction pattern can lead to information on the arrangement of atoms or ions within the crystal. This is the experimental technique to be described in this book. X-ray diffraction was first used to establish the three-dimensional arrangement of atoms in a crystal by William Lawrence Bragg in 1913 (Bragg, 1913), shortly after Wilhelm Conrad Röntgen had discovered X rays and Max von Laue had shown in 1912 that these X rays could be diffracted by crystals (Röntgen, 1895; Friedrich et al., 1912). Later, in 1927 and 1936 respectively, it was also shown that electrons and neutrons could be diffracted by crystals (Davisson and Germer, 1927; von Halban and Preiswerk, 1936; Mitchell and Powers, 1936). Bragg found from X-ray diffraction studies that, in crystals of sodium chloride, each sodium is surrounded by six equidistant chlorines and each chlorine by six equidistant sodiums. No discrete molecules of NaCl were found and therefore Bragg surmised that the crystal consisted of sodium ions and chloride ions rather than individual (noncharged) atoms (Bragg, 1913); this had been predicted earlier by William Barlow and William Jackson Pope (Barlow and Pope, 1907), but had not, prior to the research of the Braggs, been demonstrated experimentally. A decade and a half later, in 1928, Kathleen Lonsdale used X-ray diffraction methods to show that the benzene ring is a flat regular hexagon in which all carbon–carbon bonds are equal in length, rather than a ring structure that contains alternating single and double bonds (Lonsdale, 1928).Her experimental result, later confirmed by spectroscopic studies (Stoicheff, 1954), was of great significance in chemistry.

Beyond X-rays: an overview of emerging structural biology methods

2021 ◽  
Author(s):  
Jason E. Schaffer ◽  
Vandna Kukshal ◽  
Justin J. Miller ◽  
Vivian Kitainda ◽  
Joseph M. Jez
Keyword(s):  
Structure Determination ◽  
De Novo ◽  
Three Dimensional ◽  
Atomic Scale ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Main Technique

Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods.

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