Asymmetry in serial femtosecond crystallography data

Sharma, Amit; Johansson, Linda C.; Dunevall, Elin; Wahlgren, Weixiao Yuan; Neutze, Richard; Katona, Gergely

doi:10.1107/s2053273316018696

Acta Crystallogr A Found Adv

2017

DOI: 10.1107/s2053273316018696

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Asymmetry in serial femtosecond crystallography data

Amit Sharma

¹

,

Linda C. Johansson

²

,

Elin Dunevall

³

et al.

Abstract: 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 o… Show more

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Cited by 15 publications

(9 citation statements)

References 32 publications

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“…As a consequence, many of the predicted reflections will not contain any photons, and the process of integration simply produces noise, which has a Gaussian distribution rather than an exponential one. A recent paper (Sharma et al, 2017) shows this explicitly. In the Ha14 approach, we look at the distribution of the quantity I/' c (I) over all measurements on the image.…”

Section: Merging and Error Modelsmentioning

confidence: 85%

Improving signal strength in serial crystallography with DIALS geometry refinement

Brewster

¹

,

Waterman

²

,

Parkhurst

³

et al. 2018

Acta Crystallogr D Struct Biol

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Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…As a consequence, many of the predicted reflections will not contain any photons, and the process of integration simply produces noise, which has a Gaussian distribution rather than an exponential one. A recent paper (Sharma et al, 2017) shows this explicitly. In the Ha14 approach, we look at the distribution of the quantity I/' c (I) over all measurements on the image.…”

Section: Merging and Error Modelsmentioning

confidence: 85%

Improving signal strength in serial crystallography with DIALS geometry refinement

Brewster

¹

,

Waterman

²

,

Parkhurst

³

et al. 2018

Acta Crystallogr D Struct Biol

Get access via publisher Add to collection Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…However, when considering an SFX dataset in its entirety, duplicate measurements of a given Miller index form a skewed distribution peaking near zero, resulting from the many partial observations of the rocking curve tails that are low-photon count and contribute mostly noise, making it difficult to derive an 'average' intensity value that accurately represents |F h | 2 ; see especially Figs. 1 and 5 in the work by Sharma et al (2017) and Fig. 8 in the work by Kroon-Batenburg et al (2015).…”

Section: Introductionmentioning

confidence: 84%

Beyond integration: modeling every pixel to obtain better structure factors from stills

Mendez

¹

,

Bolotovsky

²

,

Bhowmick

³

et al. 2020

IUCrJ

Get access via publisher Add to collection Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…Although only a full integration into a crystallographic software package can determine the situations under which a practical benefit can be obtained from using the outlined approach, the tests here indicate that significant improvements are possible. Furthermore, the ease with which the proposed quadrature method can be adapted to a different of choice of error model is a large benefit over existing approximation methods, making it for instance possible to use experiment-specific noise models in refinement and phasing targets (Sharma et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Evaluating crystallographic likelihood functions using numerical quadratures

Zwart

¹

,

Perryman

²

2020

Acta Crystallogr D Struct Biol

Get access via publisher Add to collection Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

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