Operation of the Australian Store.Synchrotron for macromolecular crystallography

Meyer, Grischa R.; Aragão, D.; Mudie, Nathan; Caradoc-Davies, Tom T.; McGowan, Sheena; Bertling, Philip; Groenewegen, David; Quenette, Steve; Bond, Charles S.; Buckle, Ashley M.; Androulakis, G. S.

doi:10.1107/s1399004714016174

Cited by 20 publications

(20 citation statements)

References 12 publications

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“…Examples of such efforts are the NIH Big Data to Knowledge (BD2K) initiative and a number of other resources, such as http://www.proteindiffraction.org/ (USA), http://zenodo.org (Europe), https://store.synchrotron.org.au/public_data/ (Meyer et al, 2014) (Australia), and Structural Biology Data Grid https://data.sbgrid.org/ (USA). Two pioneering resources, the Joint Center for Structural Genomics (JCSG) depository and Joint Center for Structural Genomics of Infectious Diseases and Seattle Structural Genomics Center for Infectious Diseases resource, are now the part of the BD2K initiative.…”

Section: Policies Regarding Corrections Of Existing Depositsmentioning

confidence: 99%

Safeguarding Structural Data Repositories against Bad Apples

et al. 2016

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Structural biology research generates large amounts of data, some deposited in public databases/repositories, but a substantial remainder never becoming available to the scientific community. Additionally, some of the deposited data contain less or more serious errors that may bias the results of data mining. Thorough analysis and discussion of these problems is needed in order to ameliorate this situation. This note is an attempt to propose some solutions and encourage both further discussion and action on the part of the relevant organizations, in particular the Protein Data Bank and various bodies of the International Union of Crystallography.

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Section: Policies Regarding Corrections Of Existing Depositsmentioning

confidence: 99%

Safeguarding Structural Data Repositories against Bad Apples

et al. 2016

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“…All authors contributed to the manuscript. The raw X-ray diffraction data used in this experiment have been deposited at https://store.synchrotron.org.au/ (Meyer et al, 2014). These experimental data are openly available and licensed under Creative Commons Attribution 3.0 Australia (CC BY 3.0).…”

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confidence: 99%

The design and structural characterization of a synthetic pentatricopeptide repeat protein

Gully

Shah

et al. 2015

Acta Crystallogr D Biol Crystallogr

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Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to the de novo design of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.

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“…These extend the exemplary approaches of data archiving at the neutron facilities ISIS (Science & Technology Facilities Council 2011) and Institut Laue Langevin (Institut Laue Langevin 2011), and at Store. Synchrotron in Australia (Meyer et al 2014).…”

Section: Future Developmentsmentioning

confidence: 99%

Crystallography and Databases

Bruno

Gražulis

Helliwell

et al. 2017

Data Science Journal

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Crystallographic databases have existed as electronic resources for over 50 years, and have provided comprehensive archives of crystal structures of inorganic, organic, metal-organic and biological macromolecular compounds of immense value to a wide range of structural sciences. They thus serve a variety of scientific disciplines, but are all driven by considerations of accuracy, precise characterization, and potential for search, analysis and reuse. They also serve a variety of end-users in academia and industry, and have evolved through different funding and licensing models. The diversity of their operational mechanisms combined with their undisputed value as scientific research tools gives rise to a rich ecosystem. A session at SciDataCon2016 gave an overview of the largest extant crystallographic databases and their current activities and plans for the future. This review summarizes these presentations and considers them alongside other players in the field, demonstrating their variety, versatility and focus on quality and usefulness.

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Operation of the Australian Store.Synchrotron for macromolecular crystallography

Cited by 20 publications

References 12 publications

Safeguarding Structural Data Repositories against Bad Apples

Safeguarding Structural Data Repositories against Bad Apples

The design and structural characterization of a synthetic pentatricopeptide repeat protein

Crystallography and Databases

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