scholarly journals Decision letter: Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex

2016 ◽  
Keyword(s):  
Crystal Structure ◽  
Data Processing ◽  
Diffraction Data ◽  
Free Electron ◽  
Free Electron Laser ◽  
Snare Complex ◽  
X Ray ◽  
Synaptotagmin 1

scholarly journals Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Artem Y Lyubimov ◽  
Monarin Uervirojnangkoorn ◽  
Oliver B Zeldin ◽  
Qiangjun Zhou ◽  
Minglei Zhao ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Free Electron ◽  
Snare Complex ◽  
Data Sets ◽  
Free Electron Lasers ◽  
Data Set ◽  
X Ray ◽  
Density Maps ◽  
Synaptotagmin 1 ◽  
Effects Of Radiation

X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (<xref ref-type="bibr" rid="bib35">Uervirojnangkoorn et al., 2015</xref>), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (<xref ref-type="bibr" rid="bib40">Zhou et al., 2015</xref>). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models.

scholarly journals Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 560-568 ◽  
Author(s):  
Carsten Fortmann-Grote ◽  
Alexey Buzmakov ◽  
Zoltan Jurek ◽  
Ne-Te Duane Loh ◽  
Liubov Samoylova ◽  
...  
Keyword(s):  
Pulse Duration ◽  
Diffraction Data ◽  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Structural Information ◽  
X Ray ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
The Impact

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

scholarly journals Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Monarin Uervirojnangkoorn ◽  
Oliver B Zeldin ◽  
Artem Y Lyubimov ◽  
Johan Hattne ◽  
Aaron S Brewster ◽  
...  
Keyword(s):  
Data Processing ◽  
Diffraction Data ◽  
Free Electron ◽  
Biological Systems ◽  
Processing System ◽  
Data Set ◽  
X Ray ◽  
Density Maps ◽  
Beam Parameters

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

scholarly journals Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser

2019 ◽  
Vol 75 (8) ◽  
pp. 547-551 ◽  
Author(s):  
Robert J. Trachman ◽  
Jason R. Stagno ◽  
Chelsie Conrad ◽  
Christopher P. Jones ◽  
Pontus Fischer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Free Electron ◽  
Free Electron Laser ◽  
Structural Model ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Turn On

Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III–TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump–probe experiments on fluorescent RNA–small molecule complexes.

scholarly journals Data processing software suiteSITENNOfor coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA

2014 ◽  
Vol 21 (3) ◽  
pp. 600-612 ◽  
Author(s):  
Yuki Sekiguchi ◽  
Tomotaka Oroguchi ◽  
Yuki Takayama ◽  
Masayoshi Nakasako
Keyword(s):  
Data Processing ◽  
Free Electron ◽  
Free Electron Laser ◽  
Single Shot ◽  
X Ray Diffraction ◽  
X Ray ◽  
Custom Made ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Ccd Detectors

Coherent X-ray diffraction imaging is a promising technique for visualizing the structures of non-crystalline particles with dimensions of micrometers to sub-micrometers. Recently, X-ray free-electron laser sources have enabled efficient experiments in the `diffraction before destruction' scheme. Diffraction experiments have been conducted at SPring-8 Angstrom Compact free-electron LAser (SACLA) using the custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors. In the experiments, ten thousands of single-shot diffraction patterns can be collected within several hours. Then, diffraction patterns with significant levels of intensity suitable for structural analysis must be found, direct-beam positions in diffraction patterns determined, diffraction patterns from the two CCD detectors merged, and phase-retrieval calculations for structural analyses performed. A software suite namedSITENNOhas been developed to semi-automatically apply the four-step processing to a huge number of diffraction data. Here, details of the algorithm used in the suite are described and the performance for approximately 9000 diffraction patterns collected from cuboid-shaped copper oxide particles reported. Using theSITENNOsuite, it is possible to conduct experiments with data processing immediately after the data collection, and to characterize the size distribution and internal structures of the non-crystalline particles.

scholarly journals Femtosecond free-electron laser x-ray diffraction data sets for algorithm development

2012 ◽  
Vol 20 (4) ◽  
pp. 4149 ◽  
Author(s):  
Stephan Kassemeyer ◽  
Jan Steinbrener ◽  
Lukas Lomb ◽  
Elisabeth Hartmann ◽  
Andrew Aquila ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Free Electron ◽  
Free Electron Laser ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Algorithm Development ◽  
X Ray

scholarly journals Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns

2019 ◽  
Vol 75 (2) ◽  
pp. 234-241
Author(s):  
Monarin Uervirojnangkoorn ◽  
Artem Y. Lyubimov ◽  
Qiangjun Zhou ◽  
William I. Weis ◽  
Axel T. Brunger
Keyword(s):  
Diffraction Data ◽  
Free Electron ◽  
Free Electron Laser ◽  
Bravais Lattice ◽  
Data Sets ◽  
Diffraction Image ◽  
Acta Cryst ◽  
Data Set ◽  
X Ray ◽  
Automated Method

Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm–Diederichs algorithm [Brehm & Diederichs (2014), Acta Cryst. D70, 101–109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE–complexin-1–synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFEL diffraction data sets.

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