scholarly journals EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 588
Author(s):  
Yingchen Shi ◽  
Haiguang Liu
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Expectation Maximization ◽  
Expectation Maximization Algorithm ◽  
Atomic Resolution ◽  
Group Symmetry ◽  
Bravais Lattice ◽  
Free Electron Lasers ◽  
X Ray ◽  
Serial Crystallography

Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.

scholarly journals Synchrotron microcrystal native-SAD phasing at a low energy

IUCrJ ◽  
2019 ◽  
Vol 6 (4) ◽  
pp. 532-542 ◽  
Author(s):  
Gongrui Guo ◽  
Ping Zhu ◽  
Martin R. Fuchs ◽  
Wuxian Shi ◽  
Babak Andi ◽  
...  
Keyword(s):  
Data Analysis ◽  
Data Collection ◽  
Diffraction Data ◽  
De Novo ◽  
Low Energy ◽  
Anomalous Scattering ◽  
Free Electron Lasers ◽  
X Ray ◽  
Structural Evaluation ◽  
Sad Phasing

De novo structural evaluation of native biomolecules from single-wavelength anomalous diffraction (SAD) is a challenge because of the weakness of the anomalous scattering. The anomalous scattering from relevant native elements – primarily sulfur in proteins and phosphorus in nucleic acids – increases as the X-ray energy decreases toward their K-edge transitions. Thus, measurements at a lowered X-ray energy are promising for making native SAD routine and robust. For microcrystals with sizes less than 10 µm, native-SAD phasing at synchrotron microdiffraction beamlines is even more challenging because of difficulties in sample manipulation, diffraction data collection and data analysis. Native-SAD analysis from microcrystals by using X-ray free-electron lasers has been demonstrated but has required use of thousands of thousands of microcrystals to achieve the necessary accuracy. Here it is shown that by exploitation of anomalous microdiffraction signals obtained at 5 keV, by the use of polyimide wellmounts, and by an iterative crystal and frame-rejection method, microcrystal native-SAD phasing is possible from as few as about 1 200 crystals. Our results show the utility of low-energy native-SAD phasing with microcrystals at synchrotron microdiffraction beamlines.

scholarly journals The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm

IUCrJ ◽  
2014 ◽  
Vol 1 (6) ◽  
pp. 393-401 ◽  
Author(s):  
Haiguang Liu ◽  
John C.H. Spence
Keyword(s):  
Expectation Maximization ◽  
Expectation Maximization Algorithm ◽  
Group Symmetry ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Diffraction Patterns ◽  
Serial Femtosecond Crystallography ◽  
Reconstructed Model

Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these `stills'. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in theP63space group (which supports a merohedral twinning indexing ambiguity), the method is validated.

An alternative method for data analysis in serial femtosecond crystallography

2014 ◽  
Vol 70 (6) ◽  
pp. 670-676 ◽  
Author(s):  
Tao Zhang ◽  
Yang Li ◽  
Lijie Wu
Keyword(s):  
Data Analysis ◽  
Intensity Distribution ◽  
Diffraction Data ◽  
Free Electron Laser ◽  
Atomic Resolution ◽  
Diffraction Intensity ◽  
Simulation Data ◽  
X Ray ◽  
Structure Factors ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) [Chapmanet al.(2011),Nature,470, 73–77], based on the X-ray free-electron laser, is a new and powerful tool for structure analysis at atomic resolution. This study proposes an extrapolation method for diffraction data analysis on the basis of diffraction intensity distribution in reciprocal space. Results show that this new method can restore SFX simulation data to structure factors that are more consistent with the structures used in simulation.

scholarly journals Data Exploration Toolkitfor serial diffraction experiments

2015 ◽  
Vol 71 (2) ◽  
pp. 352-356 ◽  
Author(s):  
Oliver B. Zeldin ◽  
Aaron S. Brewster ◽  
Johan Hattne ◽  
Monarin Uervirojnangkoorn ◽  
Artem Y. Lyubimov ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Data Exploration ◽  
Data Sets ◽  
Significant Heterogeneity ◽  
Free Electron Lasers ◽  
X Ray ◽  
Experimental Strategy ◽  
Serial Crystallography

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the `diffraction before destruction' nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

scholarly journals X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules

2019 ◽  
Vol 88 (1) ◽  
pp. 35-58 ◽  
Author(s):  
Henry N. Chapman
Keyword(s):  
Free Electron ◽  
Conformational Dynamics ◽  
Cryogenic Cooling ◽  
X Rays ◽  
Free Electron Lasers ◽  
X Ray ◽  
Virus Particles ◽  
Structure And Dynamics ◽  
Small Crystals ◽  
Serial Crystallography

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.

scholarly journals AUSPEX: a graphical tool for X-ray diffraction data analysis

2017 ◽  
Vol 73 (9) ◽  
pp. 729-737 ◽  
Author(s):  
Andrea Thorn ◽  
James Parkhurst ◽  
Paul Emsley ◽  
Robert A. Nicholls ◽  
Melanie Vollmar ◽  
...  
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Software Tool ◽  
Data Conversion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Pixel Detectors ◽  
Graphical Tool ◽  
Data Acquisition And Processing

In this paper,AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated howAUSPEXcan be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected byAUSPEX.

D-67 High-Resolution X-ray Diffraction Data Analysis From The Partly Relaxed Semiconductor Structures

2009 ◽  
Vol 24 (2) ◽  
pp. 171-171
Author(s):  
A. Ulyanenkov ◽  
A. Benediktovitch ◽  
I. Feranchuk ◽  
B. He ◽  
H. Ress
Keyword(s):  
Data Analysis ◽  
High Resolution ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Semiconductor Structures

scholarly journals Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers

2014 ◽  
Vol 171 ◽  
pp. 393-418 ◽  
Author(s):  
S. Stern ◽  
L. Holmegaard ◽  
F. Filsinger ◽  
A. Rouzée ◽  
A. Rudenko ◽  
...  
Keyword(s):  
Free Electron ◽  
Atomic Resolution ◽  
Free Electron Lasers ◽  
Diffractive Imaging ◽  
X Ray ◽  
Isolated Molecules

scholarly journals Redetermination of the crystal structure of caesium tetrafluoridobromate(III) from single-crystal X-ray diffraction data

IUCrData ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Artem V. Malin ◽  
Sergei I. Ivlev ◽  
Roman V. Ostvald ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Point Group ◽  
Group Symmetry ◽  
Site Symmetry ◽  
X Ray Diffraction ◽  
Cation Site ◽  
X Ray ◽  
Square Planar

Caesium tetrafluoridobromate(III), CsBrF4, was crystallized in form of small blocks by melting and recrystallization. The crystal structure of CsBrF4 was redetermined from single-crystal X-ray diffraction data. In comparison with a previous study based on powder X-ray diffraction data [Ivlev et al. (2013). Z. Anorg. Allg. Chem. 639, 2846–2850], bond lengths and angles were determined with higher precision, and all atoms were refined with anisotropic displacement parameters. It was confirmed that the structure of CsBrF4 contains two square-planar [BrF4]− anions each with point group symmetry mmm, and a caesium cation (site symmetry mm2) that is coordinated by twelve fluorine atoms, forming an anticuboctahedron. CsBrF4 is isotypic with CsAuF4.

Effect of Polyaniline on Structural and Optical Characteristics of Fe3O4 and TiO2 Nanoparticles

2020 ◽  
Vol 851 ◽  
pp. 9-15
Author(s):  
Ahmad Taufiq ◽  
M.Sofiyudin Nuroni ◽  
Nurul Hidayat ◽  
ST.Ulfawanti Intan Subadra ◽  
Sunaryono ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Fourier Transform ◽  
Infrared Spectroscopy ◽  
Data Analysis ◽  
Diffraction Data ◽  
Functional Group ◽  
Bandgap Energy ◽  
X Ray Diffraction ◽  
Visible Spectroscopy ◽  
X Ray

In this work, Fe3O4 nanoparticles (NPs) were synthesized using coprecipitation method and TiO2 NPs were synthesized using sonication method. Fe3O4/polyaniline and TiO2/polyaniline nanocomposites (NCs) were synthesized using polymerization methods. The samples were characterized by X-ray diffractometer, Fourier-transform infrared spectroscopy, and ultraviolet-visible spectroscopy. The results of X-ray diffraction data analysis presented that polyaniline decreased the crystallinity of Fe3O4 and TiO2 NPs. However, the crystal structure of Fe3O4 and TiO2 NPs did not change, which successively formed the cubic spinel and the tetragonal anatase phases. Furthermore, the functional groups of Ti-O-Ti and Fe-O were detected in the wavenumber ranges of 620-580 cm-1 and 410-520 cm-1, respectively. The presence of polyaniline was also detected by the emergence of a functional group of polyaniline which also showed that there was an interaction of Fe3O4 and TiO2 NPs with polyaniline. Meanwhile, the results of UV-Vis data analysis showed that the addition of polyaniline decreased the bandgap energy of Fe3O4 and TiO2 NPs significantly from 2.186 to 2.174 eV and from 3.374 to 3.320 eV, respectively.

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