The recent surpassing of 1 million structures in the Cambridge Structural Database [1] offered a moment for celebration and an opportunity to reflect. Achieving this significant milestone is a testament to the exemplary initiatives and engagement emanating from the crystallographic community over many decades. The development of semantic representation formats [2], the cultivation of joined-up publishing workflows, and the broad adoption of standards all pre-empted the principles, guidelines and practices that have come to dominate the discourse around research data preservation and reuse today [3]. We cannot however rest on our laurels. The curation activities of organisations such as the Cambridge Crystallographic Data Centre remain of critical importance and must continue to evolve. We must ensure that our data resources remain relevant and can be readily utilised by the data-driven approaches being applied to the complex scientific problems of today.

This presentation will offer reflections on the successes of the crystallographic community that have been critical in ensuring the outputs of the past can conform to the expectations and demands of the future. It will highlight how these have enabled a wealth of structural chemistry knowledge to be applied across industry and academia to innovate and educate [4]. Additionally, it will look at the challenges and opportunities presented by an evolving research publication landscape, new experimental and computational methods, and the desire for greater reproducibility and richer reuse of structural chemistry data.

[1] Groom C. R., Bruno I. J., Lightfoot M. P. & Ward S. C. (2016). Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater. 72(2), 171.

[2] Hall S. R. & McMahon B. (2016). Data Sci. J. 15(3), 1.

[3] Wilkinson M. D., Dumontier M., Aalbersberg IjJ., et al. (2016). Sci Data. 3(1), 1.

[4] Taylor R., Wood P. A. (2019) Chem Rev. 119(16), 9427.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including > 800 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators, and students studying fundamental biology, biomedicine, biotechnology, bioengineering, and energy sciences. During the past two years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with > 40 external biodata resources. New features and resources will be described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

The Inorganic Crystal Structure Database (ICSD) has been collecting published crystal structures for more than 40 years. In addition, the database offers the structures in curated and extended form. In the process of adding a structure to the database, a series of tests are run to verify data integrity and correctness. Furthermore, the data is enriched with additional or missing information, which can help to detect possible discrepancies. Some of the procedures used will be explained here, and examples will be given to show how careful evaluation of crystallographic parameters and the addition of missing parameters improves the quality of the crystal structure entry.

The Powder Diffraction File™ (PDF®) is a comprehensive materials database containing data for inorganic materials including minerals (natural and synthetic), metals and alloys, and high-tech ceramics, as well as organic materials such as pharmaceuticals, excipients and polymers. Databases, including the PDF, that provide structural details can be used for a range of materials characterization analyses, including (but not limited to) phase identification, quantitative analysis, and structure modelling for Rietveld refinement and whole-pattern fitting. As a result, structural databases are one of the key tools used in the crystallographic community [1]. Though these databases do tend to have some common applications, they often differ in content, format, and functionality. ICDD’s PDF databases primary purpose is to serve as a quality reference tool for the powder diffraction community.

Historically, the PDF has contained entries constructed as d-spacing and intensity (d-I) reduced diffraction pattern representations for phase identification. These condensed entries reduced storage space requirements, and increased search speed capabilities. With the advancement of computer hardware and software, and the transition of the PDF to a relational database format, storage space and speed capabilities have become less limiting [2]. Over time the PDF has grown exponentially, and has evolved to where it is now common practice to construct entries of full digital patterns. In addition to being a powerful characterization database used for the analysis of single and multi-phase X-ray diffraction data, the ICDD has systematically been adding raw data digital pattern references for crystalline and non-crystalline materials since 2008; with an emphasis on excipients and polymers [3]. The addition of full digital patterns has enabled the analysis and identification of disordered and amorphous materials using a combination of the raw data pattern and d-I lists, or whole pattern similarity searching. The evolution of raw data archiving in the Powder Diffraction File will be discussed in this presentation, with emphasis on the benefits and increased capabilities for characterization of materials in both research and industrial applications including pharmaceutical, forensic, and energy sectors.

[1] Kuzel, R. and Danis, S. (2007). Mater. Struct. Chem., Biol., Phys. Technol. 14, pp.89–96.

[2] Gates-Rector, S., & Blanton, T. (2019). Powder Diffraction, 34(4), pp. 352-360.

[3] Fawcett, T., Gates-Rector, S., Gindhart, A., Rost, M., Kabekkodu, S., Blanton, J., & Blanton, T. (2019). Powder Diffraction, 34(2), pp. 164-183.

Protein Data Bank Japan (PDBj) accepts and processes regional 3D structure data of biological macromolecules since 2000. We celebrated our 20th anniversary of our regional Data-in activities last year. Our Data-out service has a much longer history, dating back to before the establishment of PDBj. The first protein structure from Asia was determined at the Institute for Protein Research (IPR) in 1971 at 4 Å [1] and a subsequent structure at 2.3 Å solved in 1973 [2] was deposited to the PDB in 1975 as the 21st entry in PDB. Based on these early contributions to the crystallographic community, IPR founded the Crystallographic Research Centre and installed several 4-circule diffractometers, and developed the Imaging Plate detectors of R-axis series later [3] together with Rigaku. In addition to above activities, IPR was assigned as the National Affiliated Centre of Cambridge Crystallographic Data Centre from 1978 and keep serving until now (http://www.protein.osaka-u.ac.jp/CSD/, Fig.1). Distribution of the PDB data from IPR started in 1979 as a regional data centre, initially by magnetic tape and later by CD-ROM, until the installation of an official mirror site of Brookhaven PDB in 1998. Since 2001, we have provided our newly developed online Data-out services freely and publicly through our own web site (https://pdbj.org; Fig.2), which includes our molecular graphics viewer, Molmil; a molecular surface database for functional sites, eF-site; and a database of protein dynamics calculated via normal mode analysis, Promode Elastic [4], and we have served since 2003 as a founding member of the worldwide PDB (https://wwpdb.org). During the COVID-19 pandemic, we have provided a COVID-19 featured page in three Asian languages (Japanese, Chinese and Korean) and have started a new service archiving raw X-ray image data directly related to deposited PDB entries (XRDa, https://xrda.pdbj.org; Fig.3) [5]. Since we already have BMRBj (formerly PDBj-BMRB) and EMPIAR-PDBj on-site, XRDa completes the regional experimental raw data archives of the related PDB, BMRB and EMDB entries from the three major experimental methods; Macromolecular Crystallography, NMR spectroscopy and 3D Electron Microscopy.

[1] Ashida, T., Ueki, T., Tsukihara, T., Sugihara, A., Takano, T. & Kakudo, M. (1971) J. Biochem. 70, 913–924. [2] Ashida, T., Tanaka, N., Yamane, T., Tsukihara, T. & Kakudo, M. (1973) J. Biochem., 73, 463–465.

[3] Sato, M., Katsube, Y. & Hayashi, K. (1993) J. Appl. Cryst., 26, 733-735.

[4] Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K., Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. & Nakamura, H. (2018) Protein Sci., 27, 95-102.

[5] Bekker, G.-J. & Kurisu, G. in preparation