scholarly journals Asymmetry in serial femtosecond crystallography data

2017 ◽  
Vol 73 (2) ◽  
pp. 93-101 ◽  
Author(s):  
Amit Sharma ◽  
Linda Johansson ◽  
Elin Dunevall ◽  
Weixiao Y. Wahlgren ◽  
Richard Neutze ◽  
...  
Keyword(s):  
Photosynthetic Reaction Center ◽  
X Ray Diffraction ◽  
Gaussian Peak ◽  
Beam Position ◽  
X Ray ◽  
Important Approach ◽  
Serial Crystallography ◽  
Blastochloris Viridis ◽  
Random Fluctuations ◽  
Serial Femtosecond Crystallography

Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of theBlastochloris viridisphotosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.

scholarly journals The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation

2019 ◽  
Vol 26 (3) ◽  
pp. 660-676 ◽  
Author(s):  
Adrian P. Mancuso ◽  
Andrew Aquila ◽  
Lewis Batchelor ◽  
Richard J. Bean ◽  
Johan Bielecki ◽  
...  
Keyword(s):  
Structure Determination ◽  
High Repetition Rate ◽  
Optical Systems ◽  
Diagnostic Tools ◽  
Imaging Method ◽  
Single Particles ◽  
X Ray ◽  
Data Rates ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation – in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.

scholarly journals Photoreversible interconversion of a phytochrome photosensory module in the crystalline state

2019 ◽  
Vol 117 (1) ◽  
pp. 300-307 ◽  
Author(s):  
E. Sethe Burgie ◽  
Jonathan A. Clinger ◽  
Mitchell D. Miller ◽  
Aaron S. Brewster ◽  
Pierre Aller ◽  
...  
Keyword(s):  
Single Crystal ◽  
Blue Light ◽  
Green Light ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Major Barrier ◽  
X Ray ◽  
Spectroscopic Analyses ◽  
Serial Femtosecond Crystallography

A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ inThermosynechococcus elongatusassembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs− Fobsdifference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.

scholarly journals Serial crystallography using automated drop dispensing

2021 ◽  
Vol 28 (5) ◽  
Author(s):  
Zhen Su ◽  
Joshua Cantlon ◽  
Lacey Douthit ◽  
Max Wiedorn ◽  
Sébastien Boutet ◽  
...  
Keyword(s):  
Free Electron Laser ◽  
Protein Crystal ◽  
Cross Contamination ◽  
X Ray ◽  
On Demand ◽  
Drop On Demand ◽  
Serial Crystallography ◽  
Cycling System ◽  
Serial Femtosecond Crystallography

Automated, pulsed liquid-phase sample delivery has the potential to greatly improve the efficiency of both sample and photon use at pulsed X-ray facilities. In this work, an automated drop on demand (DOD) system that accelerates sample exchange for serial femtosecond crystallography (SFX) is demonstrated. Four different protein crystal slurries were tested, and this technique is further improved here with an automatic sample-cycling system whose effectiveness was verified by the indexing results. Here, high-throughput SFX screening is shown to be possible at free-electron laser facilities with very low risk of cross contamination and minimal downtime. The development of this technique will significantly reduce sample consumption and enable structure determination of proteins that are difficult to crystallize in large quantities. This work also lays the foundation for automating sample delivery.

Analysis of Twin Boundary in Single Crystal of Ni-Mn-Ga Martensite Using Powder Laboratory Diffractometer

2013 ◽  
Vol 203-204 ◽  
pp. 13-16
Author(s):  
Jan Drahokoupil ◽  
Ladislav Straka ◽  
Oleg Heczko
Keyword(s):  
Single Crystal ◽  
Theoretical Calculation ◽  
Diffraction Study ◽  
Twin Boundary ◽  
Full Description ◽  
X Ray Diffraction ◽  
Beam Position ◽  
X Ray ◽  
Martensitic Microstructure ◽  
Standard Powder

The presented paper describes X-ray diffraction study of Ni-Mn-Ga modulated martensite single crystal. A standard powder laboratory diffractometer equipped with texture cradle and monocapillary was found to be suitable and sufficient tool for this type of studies. Three different scans were performed to unambiguously identify the martensitic twin variants at selected place. From this identification and with the help of theoretical calculation full description of martensitic microstructure can be determined. In addition the effect of sample displacement on beam position on sample was derived.

scholarly journals Evaluation of microflow configurations for scale inhibition and serial X-ray diffraction analysis of crystallization processes

Lab on a Chip ◽  
2020 ◽  
Vol 20 (16) ◽  
pp. 2954-2964
Author(s):  
Mark A. Levenstein ◽  
Yi-Yeoun Kim ◽  
Liam Hunter ◽  
Clara Anduix-Canto ◽  
Carlos González Niño ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Diffraction Analysis ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Scale Inhibition ◽  
Serial Crystallography

Exploration of crystal growth in microchannels led to effective scale inhibition, enabling time-resolved injector-based serial crystallography-on-a-chip.

scholarly journals FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images

2017 ◽  
Vol 50 (4) ◽  
pp. 1075-1083 ◽  
Author(s):  
Kenneth R. Beyerlein ◽  
Thomas A. White ◽  
Oleksandr Yefanov ◽  
Cornelius Gati ◽  
Ivan G. Kazantsev ◽  
...  
Keyword(s):  
Free Electron Laser ◽  
Signal To Noise Ratio ◽  
X Ray Diffraction ◽  
Signal To Noise ◽  
Monoclinic Crystal ◽  
Slight Tendency ◽  
X Ray ◽  
Serial Crystallography ◽  
Diffraction Patterns ◽  
Novel Algorithm

A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on (\overline 110) facets.

scholarly journals CrystFEL: a software suite for snapshot serial crystallography

2012 ◽  
Vol 45 (2) ◽  
pp. 335-341 ◽  
Author(s):  
Thomas A. White ◽  
Richard A. Kirian ◽  
Andrew V. Martin ◽  
Andrew Aquila ◽  
Karol Nass ◽  
...  
Keyword(s):  
Structural Information ◽  
Software Suite ◽  
X Ray ◽  
Large Numbers ◽  
Small Crystals ◽  
Serial Crystallography ◽  
Diffraction Patterns ◽  
Complicated Geometries ◽  
Serial Femtosecond Crystallography

In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.

scholarly journals Serial crystallography onin vivogrown microcrystals using synchrotron radiation

IUCrJ ◽  
2014 ◽  
Vol 1 (2) ◽  
pp. 87-94 ◽  
Author(s):  
Cornelius Gati ◽  
Gleb Bourenkov ◽  
Marco Klinge ◽  
Dirk Rehders ◽  
Francesco Stellato ◽  
...  
Keyword(s):  
Structural Model ◽  
Array Detector ◽  
Biological Macromolecules ◽  
Data Set ◽  
X Ray ◽  
Pixel Array ◽  
Structure Determinations ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography

Crystal structure determinations of biological macromolecules are limited by the availability of sufficiently sized crystals and by the fact that crystal quality deteriorates during data collection owing to radiation damage. Exploiting a micrometre-sized X-ray beam, high-precision diffractometry and shutterless data acquisition with a pixel-array detector, a strategy for collecting data from many micrometre-sized crystals presented to an X-ray beam in a vitrified suspension is demonstrated. By combining diffraction data from 80Trypanosoma bruceiprocathepsin B crystals with an average volume of 9 µm3, a complete data set to 3.0 Å resolution has been assembled. The data allowed the refinement of a structural model that is consistent with that previously obtained using free-electron laser radiation, providing mutual validation. Further improvements of the serial synchrotron crystallography technique and its combination with serial femtosecond crystallography are discussed that may allow the determination of high-resolution structures of micrometre-sized crystals.

scholarly journals Rapid sample delivery for megahertz serial crystallography at X-ray FELs

IUCrJ ◽  
2018 ◽  
Vol 5 (5) ◽  
pp. 574-584 ◽  
Author(s):  
Max O. Wiedorn ◽  
Salah Awel ◽  
Andrew J. Morgan ◽  
Kartik Ayyer ◽  
Yaroslav Gevorkov ◽  
...  
Keyword(s):  
Bragg Diffraction ◽  
X Rays ◽  
Free Electron Lasers ◽  
X Ray ◽  
Damaged Material ◽  
Optical Images ◽  
Subsequent Measurement ◽  
Serial Crystallography ◽  
Liquid Microjets ◽  
Serial Femtosecond Crystallography

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s−1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

scholarly journals Advances in Diffraction Studies of Light-Induced Transient Species in Molecular Crystals and Selected Complementary Techniques

Crystals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1345
Author(s):  
Krystyna A. Deresz ◽  
Piotr Łaski ◽  
Radosław Kamiński ◽  
Katarzyna N. Jarzembska
Keyword(s):  
Free Electron Lasers ◽  
Transient Species ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Recent Developments ◽  
Complementary Techniques ◽  
X Ray Absorption ◽  
Serial Femtosecond Crystallography ◽  
Major Emphasis

The review provides a summary of the current methods of tracing photoexcitation processes and structural dynamics in the solid state, putting major emphasis on the X-ray diffraction techniques (time-resolved Laue diffraction on synchrotron sources and time-resolved serial femtosecond crystallography on X-ray free-electron lasers). The recent developments and nowadays experimental possibilities in the field are discussed along with the data processing and analysis approaches, and illustrated with some striking literature examples of the respective successful studies. Selected complementary methods, such as ultrafast electron diffraction or time-resolved X-ray absorption spectroscopy, are briefly presented.

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