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.

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 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 On the release ofcppxfelfor processing X-ray free-electron laser images

2016 ◽  
Vol 49 (3) ◽  
pp. 1065-1072 ◽  
Author(s):  
Helen Mary Ginn ◽  
Gwyndaf Evans ◽  
Nicholas K. Sauter ◽  
David Ian Stuart
Keyword(s):  
Data Analysis ◽  
Free Electron ◽  
Free Electron Laser ◽  
Software Package ◽  
Light Sources ◽  
Data Sets ◽  
Delivery Methods ◽  
Data Set ◽  
X Ray ◽  
Software Packages

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

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.

A batch-wise non-linear fitting and analysis tool for treating large X-ray diffraction data sets

2006 ◽  
Vol 39 (2) ◽  
pp. 262-266 ◽  
Author(s):  
R. J. Davies
Keyword(s):  
Diffraction Data ◽  
Operation Mode ◽  
Large Data ◽  
Scattering Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
X Ray ◽  
Linear Fitting ◽  
Non Linear

Synchrotron sources offer high-brilliance X-ray beams which are ideal for spatially and time-resolved studies. Large amounts of wide- and small-angle X-ray scattering data can now be generated rapidly, for example, during routine scanning experiments. Consequently, the analysis of the large data sets produced has become a complex and pressing issue. Even relatively simple analyses become difficult when a single data set can contain many thousands of individual diffraction patterns. This article reports on a new software application for the automated analysis of scattering intensity profiles. It is capable of batch-processing thousands of individual data files without user intervention. Diffraction data can be fitted using a combination of background functions and non-linear peak functions. To compliment the batch-wise operation mode, the software includes several specialist algorithms to ensure that the results obtained are reliable. These include peak-tracking, artefact removal, function elimination and spread-estimate fitting. Furthermore, as well as non-linear fitting, the software can calculate integrated intensities and selected orientation parameters.

scholarly journals Quantifying instrument errors in macromolecular X-ray data sets

2010 ◽  
Vol 66 (6) ◽  
pp. 733-740 ◽  
Author(s):  
Kay Diederichs
Keyword(s):  
Data Reduction ◽  
Spindle Speed ◽  
Experimental Setup ◽  
Data Sets ◽  
Signal To Noise ◽  
Instrument Error ◽  
Acta Cryst ◽  
Data Set ◽  
X Ray ◽  
The Stability

An indicator which is calculated after the data reduction of a test data set may be used to estimate the (systematic) instrument error at a macromolecular X-ray source. The numerical value of the indicator is the highest signal-to-noise [I/σ(I)] value that the experimental setup can produce and its reciprocal is related to the lower limit of the mergingRfactor. In the context of this study, the stability of the experimental setup is influenced and characterized by the properties of the X-ray beam, shutter, goniometer, cryostream and detector, and also by the exposure time and spindle speed. Typical values of the indicator are given for data sets from the JCSG archive. Some sources of error are explored with the help of test calculations usingSIM_MX[Diederichs (2009),Acta Cryst.D65, 535–542]. One conclusion is that the accuracy of data at low resolution is usually limited by the experimental setup rather than by the crystal. It is also shown that the influence of vibrations and fluctuations may be mitigated by a reduction in spindle speed accompanied by stronger attenuation.

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 Poisson errors and adaptive rebinning in X-ray powder diffraction data

2018 ◽  
Vol 33 (4) ◽  
pp. 266-269 ◽  
Author(s):  
Marcus H. Mendenhall
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Data Sets ◽  
Powder Diffraction Data ◽  
Data Set ◽  
X Ray ◽  
Short Summary ◽  
Correct Assignment ◽  
Wide Range ◽  
Diffraction Patterns

This work provides a short summary of techniques for formally-correct handling of statistical uncertainties in Poisson-statistics dominated data, with emphasis on X-ray powder diffraction patterns. Correct assignment of uncertainties for low counts is documented. Further, we describe a technique for adaptively rebinning such data sets to provide more uniform statistics across a pattern with a wide range of count rates, from a few (or no) counts in a background bin to on-peak regions with many counts. This permits better plotting of data and analysis of a smaller number of points in a fitting package, without significant degradation of the information content of the data set. Examples of the effect of this on a diffraction data set are given.

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