Crystal structure of the second extracellular domain of human tetraspanin CD9: twinning and diffuse scattering

Neviani, Viviana; Lutz, Martin; Oosterheert, Wout; Gros, Piet; Kroon-Batenburg, Loes M. J.

doi:10.1107/s2414314622008525

Cited by 4 publications

(3 citation statements)

References 8 publications

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“…The output format for the 3D map is compatible with software developed for viewing electron density. The EVAL suite of programs (De Klijn et al, 2019;Schreurs et al, 2010) should be used when greater detail is needed, for instance to visualize sharp streaks or satellite reflections from modulated structures (Neviani et al, 2022). EVAL implements pixel splitting to produce densely sampled maps, and it includes an array of additional tools for analyzing non-standard diffraction data.…”

Section: Data Processing Softwarementioning

confidence: 99%

Processing macromolecular diffuse scattering data

Meisburger

Ando

2023

Preprint

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Diffuse scattering is a powerful technique to study disorder and dynamics of macromolecules at atomic resolution. Although diffuse scattering is always present in diffraction images from macromolecular crystals, the signal is weak compared with Bragg peaks and background, making it a challenge to visualize and measure accurately. Recently, this challenge has been addressed using the reciprocal space mapping technique, which leverages ideal properties of modern X-ray detectors to reconstruct the complete three-dimensional volume of continuous diffraction from diffraction images of a crystal (or crystals) in many different orientations. This chapter will review recent progress in reciprocal space mapping with a particular focus on the strategy implemented in the mdx-lib and mdx2 software packages. The chapter concludes with an introductory data processing tutorial using Python packages DIALS, NeXpy, and mdx2.

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Section: Data Processing Softwarementioning

confidence: 99%

Processing macromolecular diffuse scattering data

Meisburger

Ando

2023

Preprint

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“…Figure 1Upload page on Zenodo with the data items as filled in for the first Raw Data Letter(Neviani et al, 2022). (a) The raw data file chosen will be uploaded after pressing the 'Start upload' button.…”

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confidence: 99%

Making your raw data available to the macromolecular crystallography community

Kroon-Batenburg

2023

Acta Cryst Sect F

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A recent editorial in the IUCr macromolecular crystallography journals [Helliwell et al. (2019), Acta Cryst. D75, 455–457] called for the implementation of the FAIR data principles. This implies that the authors of a paper that describes research on a macromolecular structure should make their raw diffraction data available. Authors are already used to submitting the derived data (coordinates) and the processed data (structure factors, merged or unmerged) to the PDB, but may still be uncomfortable with making the raw diffraction images available. In this paper, some guidelines and instructions on depositing raw data to Zenodo are given.

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“…For the first letters published, we generated complete and consistent imgCIF files using the CBF laboratory axis system. For the macromolecular letter (Neviani et al, 2022), we used a Python script written by Fabio Dall'Antonia and Julian Ho ¨rsch (European XFEL) to convert the metadata information from a Nexus/HDF5 master file into CBF/imgCIF. This particular Diamond Light Source Nexus/HDF5 (meta)data follows the 'Gold Standard' defined by the HDRMX working group (Bernstein et al, 2020).…”

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confidence: 99%

IUCrData launches Raw Data Letters

Kroon-Batenburg¹,

Helliwell²,

Hester³

2022

IUCrData

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IUCrData, the peer-reviewed open-access data publication from the International Union of Crystallography (IUCr), is launching a new section -Raw Data Letters. This is a collaborative innovation of IUCr Journals with the IUCr Committee on Data. Future raw data sets will become increasingly large and no one group will be able to analyze all of the scientific content in a timely manner. As already occurs in other scientific disciplines (e.g. astronomy, particle physics) others will need to have access to raw crystallographic data sets so that open-science-based research can proceed at a rapid pace. However, proper credit needs to be attributed fairly among those who design experiments and collect data, and those who subsequently use the data to establish new results.With these points in mind, the new section will publish short descriptions of crystallographic raw data sets from X-ray, neutron or electron diffraction experiments, in the biological, chemical, materials science or physics fields, and provide a persistent link to the location of the raw data. The letters in this section will describe interesting features in raw data sets, allowing researchers to attract attention to particular aspects of the data that could be of interest to methods and software developers for purposes such as reanalysis by newer methods or may be relevant to the structural interpretation. We envisage different types of Raw Data Letters. The structure could have been solved and published elsewhere, but the letter describes interesting features that were observed but ignored in the original structure determination. The letter could describe remarkable features but no attempt is made as to their interpretation; in this way the data attract attention and the original authors get credit for their work. The raw data described in a letter show Bragg reflections to a reasonable resolution but the structure could not be solved. Again the authors would get credit for their work. Also letters describing the reuse of publicly available data by improved methods are welcome. In general, publication in Raw Data Letters promotes data retrieval by other scientists and will enhance visibility of the data. Raw Data Letters support Open Science policies: no research data should be lost but should be made available to the research community according to the FAIR principles, for which the correctness and completeness of the metadata are crucial, and these will be central to the reviewing process.Science funders and policy makers are working increasingly towards the Open Science model to make science useful for society. Good scholarship demands openness and transparency of protocols and scientific results as well as proper data management and validation of scientific knowledge. Many open science platforms have seen the light, e.g. the OpenAIRE project (https://www.openaire.eu) and the European Open Science Cloud (EOSC, Jones, 2015) promoting the sharing of data. Guidelines for proper data management are described in The FAIR principles for scientific data m...

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Crystal structure of the second extracellular domain of human tetraspanin CD9: twinning and diffuse scattering

Cited by 4 publications

References 8 publications

Processing macromolecular diffuse scattering data

Processing macromolecular diffuse scattering data

Making your raw data available to the macromolecular crystallography community

IUCrData launches Raw Data Letters

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