Control of strain in subgrains of protein crystals by the introduction of grown-in dislocations

2021 ◽  
Vol 77 (5) ◽  
pp. 599-605
Author(s):  
Haruhiko Koizumi ◽  
Satoshi Uda ◽  
Ryo Suzuki ◽  
Masaru Tachibana ◽  
Kenichi Kojima ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Local Strain ◽  
Glucose Isomerase ◽  
Crystal Quality ◽  
Protein Crystals ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Equal Thickness

It is important to reveal the exact cause of poor diffractivity in protein crystals in order to determine the accurate structure of protein molecules. It is shown that there is a large amount of local strain in subgrains of glucose isomerase crystals even though the overall crystal quality is rather high, as shown by clear equal-thickness fringes in X-ray topography. Thus, a large stress is exerted on the subgrains of protein crystals, which could significantly lower the resistance of the crystals to radiation damage. It is also demonstrated that this local strain can be reduced through the introduction of dislocations in the crystal. This suggests that the introduction of dislocations in protein crystals can be effective in enhancing the crystal quality of subgrains of protein crystals. By exploiting this effect, the radiation damage in subgrains could be decreased, leading to the collection of X-ray diffraction data sets with high diffractivity.

scholarly journals Evaluation of crystal quality of thin protein crystals based on the dynamical theory of X-ray diffraction

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 761-766
Author(s):  
Marina Abe ◽  
Ryo Suzuki ◽  
Kenichi Kojima ◽  
Masaru Tachibana
Keyword(s):  
Imaging Techniques ◽  
Glucose Isomerase ◽  
Dynamical Theory ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
Rocking Curve ◽  
Dynamical Diffraction ◽  
X Ray ◽  
Equal Thickness

Knowledge of X-ray diffraction in macromolecular crystals is important for not only structural analysis of proteins but also diffraction physics. Dynamical diffraction provides evidence of perfect crystals. Until now, clear dynamical diffraction in protein crystals has only been observed in glucose isomerase crystals. We wondered whether there were other protein crystals with high quality that exhibit dynamical diffraction. Here we report the observation of dynamical diffraction in thin ferritin crystals by rocking-curve measurement and imaging techniques such as X-ray topography. It is generally known that in the case of thin crystals it is difficult to distinguish whether dynamical diffraction occurs from only rocking-curve profiles. Therefore, our results clarified that dynamical diffraction occurs in thin protein crystals because fringe contrasts similar to Pendellösung fringes were clearly observed in the X-ray topographic images. For macromolecular crystallography, it is hard to obtain large crystals because they are difficult to crystallize. For thin crystals, dynamical diffraction can be demonstrated by analysis of the equal-thickness fringes observed by X-ray topography.

Recrystallization: a method to improve the quality of protein crystals

2015 ◽  
Vol 48 (3) ◽  
pp. 758-762 ◽  
Author(s):  
Hai Hou ◽  
Yue Liu ◽  
Bo Wang ◽  
Fan Jiang ◽  
Hao-Ran Tao ◽  
...  
Keyword(s):  
Crystal Quality ◽  
Proteinase K ◽  
Protein Crystals ◽  
Structural Determination ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Quality Protein ◽  
Before And After

The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.

Annealing Time Dependence on 1.5μm Photoluminescence of Laser-Ablated β-FeSi2

2005 ◽  
Vol 891 ◽  
Author(s):  
Shin-ichiro Uekusa ◽  
Kunitoshi Aoki ◽  
Mohammad Zakir Hossain ◽  
Tomohiro Fukuda ◽  
Noboru Miura
Keyword(s):  
Thin Films ◽  
High Temperature ◽  
Thermal Diffusion ◽  
Annealing Time ◽  
Crystal Quality ◽  
Photoluminescence Intensity ◽  
X Ray Diffraction ◽  
X Ray ◽  
Long Time

ABSTRACTWe prepared β-FeSi2 thin-films by using a Pulsed Laser Deposition (PLD) method and succeeded to observe photoluminescence (PL) around 1.5 μm corresponding to β-FeSi2 band from the long-time and high-temperature annealed β-FeSi2 thin-films. The β-FeSi2 thin-films were ablated on Si(111) substrates heated at 550°C. After ablation, long-time and high-temperature thermal annealing was performed in order to improve the crystal-quality. Annealing times were 5, 10, 20 and 40 hrs, and annealing temperature was kept at 900 °C. Crystallinity was evaluated by an X-ray diffraction (XRD) measurement. We have observed eminent improvement on crystal-quality of β-FeSi2 thin-films. Annealed samples show (220) or (202) X-ray diffraction signals of β-FeSi2 and the full width at half maximum (FWHM) of these peaks were 0.27° although the thickness of the samples decreased with annealing time. Thermal-diffusion of Si atoms was observed from substrate to thin-films. Fe atoms in the ablated thin-films also diffused into the substrate. The relationship between the thickness of β-FeSi2 thin-films and the thermal-diffusion were investigated with rutherford backscattering (RBS) measurement. Maximum photoluminescence intensity around 1.5 μm was observed from the thickest β-FeSi2 thin-film with only 5 hrs annealing.

XRD Instrument Sensitivity Results from a Round Robin Study

1991 ◽  
Vol 35 (A) ◽  
pp. 333-340 ◽  
Author(s):  
W.N. Schreiner ◽  
R. Jenkins ◽  
P.F. Dismore
Keyword(s):  
Diffraction Data ◽  
Round Robin ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Diffraction Intensity ◽  
Generic Type ◽  
X Ray ◽  
The Past ◽  
Instrument Sensitivity

During the course of the past ten years the International Centre for Diffraction Data has sponsored a number of “Round Robin” tests to evaluate the quality of experimental X-ray diffraction data [1-5]. The latest of this series, called the Instrument Parameter Round Robin, was designed to evaluate, among other things, relative angularly-dependent sensitivity differences between diffractometers. Previous experiments have indicated that even perfectly aligned diffractometers of the same generic type, do not necessarily give the same set of relative intensities. One objective of the round robin was to quantify the magnitude of the experimental differences between data sets, and to demonstrate a means for external calibration of diffractometers, so that digitized diffraction intensity data obtained from different instruments could be directly compared.

scholarly journals Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 501 ◽  
Author(s):  
Li ◽  
Yan ◽  
Liu ◽  
Wu ◽  
Liu ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
High Quality Protein

We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.

Study of diffraction data sets using factor analysis: a new technique for comparing mineralogical and geochemical data and rapid diagnostics of the mineral composition of large collections of rock samples

2019 ◽  
Vol 34 (S1) ◽  
pp. S59-S70 ◽  
Author(s):  
Ekaterina Fomina ◽  
Evgeniy Kozlov ◽  
Svetlana Ivashevskaja
Keyword(s):  
Geochemical Data ◽  
Chemical Compositions ◽  
Data Sets ◽  
Rapid Diagnostics ◽  
X Ray Diffraction ◽  
X Ray ◽  
Short Period ◽  
Diffraction Patterns ◽  
A New Technique

This paper presents an example of comparing geochemical and mineralogical data by means of the statistical analysis of the X-ray diffraction patterns and the chemical compositions of bulk samples. The proposed methodology was tested on samples of metasomatic rocks from two geologically different objects. Its application allows us to mathematically identify all the main, secondary and some accessory minerals, to qualitatively estimate the contents of these minerals, as well as to assess their effect on the distribution of all petrogenic and investigated trace elements in a short period of time at the earliest stages of the research. We found that the interpretation of the results is significantly influenced by the number of samples studied and the quality of diffractograms.

On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds

2018 ◽  
Vol 51 (4) ◽  
pp. 1094-1101 ◽  
Author(s):  
Yunchen Wang ◽  
Taimin Yang ◽  
Hongyi Xu ◽  
Xiaodong Zou ◽  
Wei Wan
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structural Models ◽  
Electron Diffraction Data ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Continuous Rotation

The continuous rotation electron diffraction (cRED) method has the capability of providing fast three-dimensional electron diffraction data collection on existing and future transmission electron microscopes; unknown structures could be potentially solved and refined using cRED data collected from nano- and submicrometre-sized crystals. However, structure refinements of cRED data using SHELXL often lead to relatively high R1 values when compared with those refined against single-crystal X-ray diffraction data. It is therefore necessary to analyse the quality of the structural models refined against cRED data. In this work, multiple cRED data sets collected from different crystals of an oxofluoride (FeSeO3F) and a zeolite (ZSM-5) with known structures are used to assess the data consistency and quality and, more importantly, the accuracy of the structural models refined against these data sets. An evaluation of the precision and consistency of the cRED data by examination of the statistics obtained from the data processing software DIALS is presented. It is shown that, despite the high R1 values caused by dynamical scattering and other factors, the refined atomic positions obtained from the cRED data collected for different crystals are consistent with those of the reference models refined against single-crystal X-ray diffraction data. The results serve as a reference for the quality of the cRED data and the achievable accuracy of the structural parameters.

Study of Depth-Dependent Tetragonal Distortion of GaN Epilayer with Tri-Layer AlGaN Interlayer Growth on Si(111)

2011 ◽  
Vol 413 ◽  
pp. 11-17 ◽  
Author(s):  
Bin Feng Ding ◽  
Yong Quan Chai
Keyword(s):  
Chemical Vapor ◽  
Crystal Quality ◽  
Tetragonal Distortion ◽  
Organic Chemical ◽  
X Ray Diffraction ◽  
Near Surface ◽  
X Ray ◽  
Metal Organic ◽  
Organic Chemical Vapor Deposition

A GaN epilayer with tri-layer AlGaN interlayer grown on Si (111) by metal-organic chemical vapor deposition (MOCVD) method was discussed by synchrotron radiation x-ray diffraction (SRXRD) and Rutherford backscattering (RBS)/C. The crystal quality of the epilayer is very good with a χmin=2.1%. According to the results of the θ-2θ scan of GaN(0002) and GaN(1122), the epilayer elastic strains in perpendicular and parallel directions were calculated respectively to be-0.019% and 0.063%. By the angular scan using RBS/C around a symmetric [0001] axis and an asymmetric [1213] axis in the (1010) plane of the GaN layer, the tetragonal distortion (eT ) were determined to be 0.09%. This result coincides with that from SRXRD perfectly. The strain decreases gradually towards the near-surface layer, which will avoid the film cracks efficiently and improve the crystal quality of the GaN epilayer remarkably.

scholarly journals MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines

2015 ◽  
Vol 71 (11) ◽  
pp. 2328-2343 ◽  
Author(s):  
Ulrich Zander ◽  
Gleb Bourenkov ◽  
Alexander N. Popov ◽  
Daniele de Sanctis ◽  
Olof Svensson ◽  
...  
Keyword(s):  
Hierarchical Cluster ◽  
Data Sets ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Partial Data ◽  
Final Data ◽  
Dispersion Technique

Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.

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