scholarly journals Redetermination of the first unknown protein MicroED structure by high resolution X-ray diffraction

2021 ◽  
Author(s):  
Hongyi Xu ◽  
Xiaodong Zou ◽  
Martin Högbom ◽  
Hugo Lebrette
Keyword(s):  
Protein Structures ◽  
Real Life ◽  
Relevant Information ◽  
Binding Pocket ◽  
X Ray Diffraction ◽  
X Ray ◽  
Biologically Relevant ◽  
Atomic Structures ◽  
Unknown Protein ◽  
Wide Range

Microcrystal electron diffraction (MicroED) has the potential to considerably impact the field of structural biology. Indeed, the method can solve atomic structures of a wide range of molecules, beyond the reach of single particle cryo-electron microscopy, exploiting crystals too small for X-ray diffraction (XRD) even using X-ray free-electron lasers. However, until the first unknown protein structure – a R2-like ligand binding oxidase from Sulfolobus acidocaldarius (SaR2lox) – was recently solved at 3.0 Å resolution, MicroED had only been used to study known protein structures previously obtained by XRD. Here, after adapting sample preparation protocols, the structure of the SaR2lox protein originally solved by MicroED was redetermined by XRD at 2.1 Å resolution. In light of the higher resolution XRD data and taking into account experimental differences of the methods, the quality of the MicroED structure is examined. The analysis demonstrates that MicroED provided an overall accurate model, revealing biologically relevant information specific to SaR2lox, such as the absence of an ether cross-link, but did not allow to detect the presence of a ligand visible by XRD in the protein binding pocket. Furthermore, strengths and weaknesses of MicroED compared to XRD are discussed in the perspective of this real-life protein example. The study provides fundaments to help MicroED become a method of choice for solving novel protein structures.

Hrem Studies of Rapidly Solidified Ni-Fe-Al-B Shape Memory Alloys.

1991 ◽  
Vol 246 ◽  
Author(s):  
R. Pērez ◽  
J. A. Juārez-Islas ◽  
P. Johansson ◽  
M. Wallin ◽  
S. J. Savage
Keyword(s):  
Shape Memory ◽  
Martensite Transformation ◽  
Melt Spinning ◽  
Image Contrast ◽  
X Ray Diffraction ◽  
Recoverable Strain ◽  
X Ray ◽  
Atomic Structures ◽  
Wide Range ◽  
Rapidly Solidified

AbstractA series of (NixFeyAlz)0.9983B0.0017 (where x=58-60, y=13-15 and z=26-28, in at%) alloys have been rapidly solidified by - melt spinning. The ribbons have been characterized by HREM, DSC, X-ray diffraction and recoverable strain measurements. The as-cast alloys exhibit excellent bend ductility (in contrast to B2 type alloys conventionally cast) and a wide range of transformation temperatures: Ms=244-466 K, Mf=200-395K, As=236-427K and Af=262-526K. X-ray diffraction shows the presence of β (NiAl), β′ (NiAl), γ (Ni3Al), γ′ (Ni3A1), Ni and other phases such as Fe3Al, FeAl, FeNi and Al5Fe2. It is the β- β′ diffusionless transformation which is responsible for the shape memory effect. The results obtained by transmission electron microscopy (TEM) show two different types of crystalline grains. In one case, the grains have a high density of twins which are the fingerprints of the martensite transformation. However, other areas in the specimen show crystalline grains with very poor image contrast due to the transformation from β′ -β. There are also sections in the specimens with domains of both crystalline sgrains in coexistance. Both crystalline grains have large amounts of precipitates. In the β′ (NiAl) phase the size of the precipitates range fron lnm to lOnm. In the γ (Ni3Al) phase large precipitates (20nm) can be found. Some of them display pentagonal shapes which resemble the image contrast obtained in the TEM for small icosahedral metallic particles. Experimental evidence is also obtained on different habit or twin planes. HREM images from the twinned areas suggest diferent kinds of atomic structures for the parent and martensite crystalline sections. These results give some insights into the nature of the martensite transformation.

scholarly journals Multidimensional Ln-Aminophthalate Photoluminescent Coordination Polymers

Materials ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1786
Author(s):  
Carla Queirós ◽  
Chen Sun ◽  
Ana M. G. Silva ◽  
Baltazar de Castro ◽  
Juan Cabanillas-Gonzalez ◽  
...  
Keyword(s):  
Water Content ◽  
Coordination Polymers ◽  
Metal Ion ◽  
Low Cost ◽  
Microwave Assisted Synthesis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Ft Ir ◽  
Ft Ir Spectroscopy

The development of straightforward reproducible methods for the preparation of new photoluminescent coordination polymers (CPs) is an important goal in luminescence and chemical sensing fields. Isophthalic acid derivatives have been reported for a wide range of applications, and in addition to their relatively low cost, have encouraged its use in the preparation of novel lanthanide-based coordination polymers (LnCPs). Considering that the photoluminescent properties of these CPs are highly dependent on the existence of water molecules in the crystal structure, our research efforts are now focused on the preparation of CP with the lowest water content possible, while considering a green chemistry approach. One- and two-dimensional (1D and 2D) LnCPs were prepared from 5-aminoisophthalic acid and Sm3+/Tb3+ using hydrothermal and/or microwave-assisted synthesis. The unprecedented LnCPs were characterized by single-crystal X-ray diffraction (SCRXD), powder X-ray diffraction (PXRD), Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM), and their photoluminescence (PL) properties were studied in the solid state, at room temperature, using the CPs as powders and encapsulated in poly(methyl methacrylate (PMMA) films, envisaging the potential preparation of devices for sensing. The materials revealed interesting PL properties that depend on the dimensionality, metal ion, co-ligand used and water content.

Local atomic structure in tetragonal pure ZrO2nanopowders

2010 ◽  
Vol 43 (2) ◽  
pp. 227-236 ◽  
Author(s):  
Leandro M. Acuña ◽  
Diego G. Lamas ◽  
Rodolfo O. Fuentes ◽  
Ismael O. Fábregas ◽  
Márcia C. A. Fantini ◽  
...  
Keyword(s):  
Tetragonal Phase ◽  
Local Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Crystallite Sizes ◽  
Exafs Study ◽  
The Difference ◽  
X Ray Absorption ◽  
Good Agreement

The local atomic structures around the Zr atom of pure (undoped) ZrO2nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr—O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye–Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to thezdirection; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

scholarly journals Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

2013 ◽  
Vol 6 (1) ◽  
pp. 308 ◽  
Author(s):  
Mikael Elias ◽  
Dorothee Liebschner ◽  
Jurgen Koepke ◽  
Claude Lecomte ◽  
Benoit Guillot ◽  
...  
Keyword(s):  
High Resolution ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Diffraction Structure

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 273 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

2018 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals Theoretical study of the properties of X-ray diffraction moiré fringes. II. Illustration of angularly integrated moiré images

2019 ◽  
Vol 75 (4) ◽  
pp. 610-623
Author(s):  
Jun-ichi Yoshimura
Keyword(s):  
Incident Wave ◽  
Angular Width ◽  
X Ray Diffraction ◽  
Experimental Conditions ◽  
Acta Cryst ◽  
Low Contrast ◽  
X Ray ◽  
Moiré Fringes ◽  
Wide Range ◽  
Fringe Patterns

Using a theory of X-ray diffraction moiré fringes developed in a previous paper, labelled Part I [Yoshimura (2015). Acta Cryst. A71, 368–381], the X-ray moiré images of a silicon bicrystal having a weak curvature strain and an interspacing gap, assumed to be integrated for an incident-wave angular width, are simulation-computed over a wide range of crystal thicknesses and incident-wave angular width, likely under practical experimental conditions. Along with the simulated moiré images, the graphs of characteristic quantities on the moiré images are presented for a full understanding of them. The treated moiré images are all of rotation moiré. Mo Kα1 radiation and the 220 reflection were assumed in the simulation. The results of this simulation show that fringe patterns, which are significantly modified from simple straight fringes of rotation moiré, appear in some ranges of crystal thicknesses and incident-wave angular width, due to a combined effect of Pendellösung oscillation and an added phase difference from the interspacing gap, under the presence of a curvature strain. The moiré fringes which slope to the perpendicular direction to the diffraction vector in spite of the assumed condition of rotation moiré, and fringe patterns where low-contrast bands are produced with a sharp bend of fringes arising along the bands are examples of the modified fringe pattern. This simulation study provides a wide theoretical survey of the type of bicrystal moiré image produced under a particular condition.

scholarly journals Charge Compensation in Europium-Doped Hafnia Nanoparticles: Solvothermal Synthesis and Colloidal Dispersion

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1042
Author(s):  
Xavier H. Guichard ◽  
Francesco Bernasconi ◽  
Alessandro Lauria
Keyword(s):  
Low Temperature ◽  
Hafnium Oxide ◽  
Aqueous Media ◽  
Charge Compensation ◽  
Colloidal Dispersion ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Direct Formation ◽  
Enhanced Luminescence

Effective charge compensation of europium in hafnium oxide nanoparticles was achieved at low temperature, allowing high doping incorporation (up to 6 at.%) and enhanced luminescence. The efficiency of the incorporation and charge compensation was confirmed by scanning electron microscope energy dispersive X-ray spectroscopy and powder X-ray diffraction measurements. Despite the known polymorphism of hafnium oxide, when doped to a concentration above 3 at.%, only the pure monoclinic phase was observed up to 6 at.% of europium. Furthermore, the low-temperature solvothermal route allowed the direct formation of stable dispersions of the synthesized material over a wide range of concentrations in aqueous media. The dispersions were studied by diffuse light scattering (DLS) to evaluate their quality and by photoluminescence to investigate the incorporation of the dopants into the lattice.

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