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 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 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.

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 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 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.

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

Determination of depth profiles from X-ray diffraction data

1993 ◽  
Vol 8 (2) ◽  
pp. 122-126 ◽  
Author(s):  
Paul Predecki
Keyword(s):  
Diffraction Data ◽  
Direct Method ◽  
Sample Surface ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Depth Profiles ◽  
A Direct Method

A direct method is described for determining depth profiles (z-profiles) of diffraction data from experimentally determined τ-profiles, where z is the depth beneath the sample surface and τ is the 1/e penetration depth of the X-ray beam. With certain assumptions, the relation between these two profile functions can be expressed in the form of a Laplace transform. The criteria for fitting experimental τ-data to functions which can be utilized by the method are described. The method was applied to two τ-data sets taken from the literature: (1) of residual strain in an A1 thin film and (2) of residual stress in a surface ground A12O3/5vol% TiC composite. For each data set, it was found that the z-profiles obtained were of two types: oscillatory and nonoscillatory. The nonoscillatory profiles appeared to be qualitatively consistent for a given data set. The oscillatory profiles were considered to be not physically realistic. For the data sets considered, the nonoscillatory z-profiles were found to lie consistently above the corresponding τ-profiles, and to approach the τ-profiles at large z, as expected from the relation between the two.

X-Ray Powder Diffraction Study of 2,2′,2″ triamino-triethylamine-Ni(II)-di-thiocyanate by Transmission PSD Diffractometer and Rietveld Techniques

1991 ◽  
Vol 6 (3) ◽  
pp. 166-169
Author(s):  
Britta Lundtoft ◽  
Svend Erik Rasmussen
Keyword(s):  
Diffraction Study ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Internal Standard ◽  
Data Sets ◽  
Powder Diffraction Data ◽  
Data Set ◽  
X Ray ◽  
Lattice Constants ◽  
Deep Blue

AbstractX-Ray powder diffraction data for the compound 2,2′,2″-triamino-triethylamine-Ni(II)-di-thiocyanate were obtained by transmission diffractometric methods at 20°C - 22°C. Two data sets were collected with CuKα1 radiation (λ = 1.54056 Å) one with Si as an internal standard (a = 5.430825 Å) and one without.The deep blue crystals are orthorhombic of space group P212121. Peak positions were corrected by aid of the Si peaks in the first data set. Refinements of lattice constants from indexed reflections yielded the following values: a = 10.8524(18) Å; b = 14.7249(16) Å; c = 8.6511(11) Å; Dx = 1.542 Mg/m3. The second data set was used for a Rietveld refinement. The lattice constants obtained by this method are: a = 10.8451(5) Å; b = 14.7148 Å; c = 8.6447(4) Å.

Sign in / Sign up

Export Citation Format

Share Document