scholarly journals Recent developments in CrystFEL

2016 ◽  
Vol 49 (2) ◽  
pp. 680-689 ◽  
Author(s):  
Thomas A. White ◽  
Valerio Mariani ◽  
Wolfgang Brehm ◽  
Oleksandr Yefanov ◽  
Anton Barty ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Lasers ◽  
Software Suite ◽  
X Ray ◽  
Processing Data ◽  
Recent Developments ◽  
Serial Crystallography

CrystFEL is a suite of programs for processing data from `serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve `indexing ambiguities' and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics.

scholarly journals Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130590 ◽  
Author(s):  
Jan Kern ◽  
Johan Hattne ◽  
Rosalie Tran ◽  
Roberto Alonso-Mori ◽  
Hartawan Laksmono ◽  
...  
Keyword(s):  
Free Electron ◽  
Water Oxidation ◽  
Spectroscopic Studies ◽  
Free Electron Lasers ◽  
Software Suite ◽  
X Ray ◽  
Methods Development ◽  
Wide Range ◽  
Linac Coherent Light Source ◽  
Spectroscopy Studies

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel . This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.

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 Cryo-coherent diffractive imaging of biological samples with X-ray free-electron lasers

2016 ◽  
Vol 72 (2) ◽  
pp. 177-178
Author(s):  
Huaidong Jiang
Keyword(s):  
Biological Samples ◽  
Free Electron ◽  
Free Electron Laser ◽  
Free Electron Lasers ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
Recent Developments

Recent developments in the imaging of biological samples using the X-ray free-electron laser at the SACLA facility are highlighted.

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 Reducing sample consumption for serial crystallography using acoustic drop ejection

2019 ◽  
Vol 26 (5) ◽  
pp. 1820-1825 ◽  
Author(s):  
Bradley Davy ◽  
Danny Axford ◽  
John H. Beale ◽  
Agata Butryn ◽  
Peter Docker ◽  
...  
Keyword(s):  
Efficient Method ◽  
Free Electron ◽  
Crystal Quality ◽  
Free Electron Lasers ◽  
Fixed Target ◽  
X Ray ◽  
Essential Aspect ◽  
Time Usage ◽  
Order Of Magnitude ◽  
Serial Crystallography

Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry.

scholarly journals Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 628
Author(s):  
Suraj Pandey ◽  
Ishwor Poudyal ◽  
Tek Narsingh Malla
Keyword(s):  
Free Electron ◽  
Reaction Dynamics ◽  
Reaction Coordinate ◽  
Biological Macromolecules ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Recent Developments ◽  
Serial Femtosecond Crystallography

With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.

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 Current status and future opportunities for serial crystallography at MAX IV Laboratory

2020 ◽  
Vol 27 (5) ◽  
pp. 1095-1102
Author(s):  
Anastasya Shilova ◽  
Hugo Lebrette ◽  
Oskar Aurelius ◽  
Jie Nan ◽  
Martin Welin ◽  
...  
Keyword(s):  
Free Electron ◽  
Room Temperature ◽  
High Viscosity ◽  
Current Status ◽  
Free Electron Lasers ◽  
X Ray ◽  
X Ray Crystallography ◽  
Injection Methods ◽  
Serial Crystallography ◽  
Presentation Methods

Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at  MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports – silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.

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