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To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
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The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
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X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
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Ionic crystals consist of two or more different kinds of ions that usually have different sizes. The packing of these ions into a crystal structure is more complex than the packing of metal atoms that are the same size.
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Crystallization is a phase transformation process in which crystals are precipitated from a supersaturated solution or formed from other sources. During crystallization, atoms or molecules arrange themselves into a well-defined, rigid crystal lattice to minimize energy.
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Microcrystallography of Protein Crystals and In Cellulo Diffraction
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Validation of the Crystallography Open Database using the Crystallographic Information Framework.

Antanas Vaitkus1, Andrius Merkys1, Saulius Gražulis1,2

  • 1Department of Protein-DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania.

Journal of Applied Crystallography
|May 6, 2021
PubMed
Summary
This summary is machine-generated.

Data curation in the Crystallography Open Database (COD) is enhanced by formal validation using the Crystallographic Information Framework (CIF). This process improves data quality and aids in ontology development.

Keywords:
CIF dictionaryCIF validationCrystallographic Information FrameworkCrystallography Open DatabaseDDLm

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Area of Science:

  • Crystallography
  • Data Science
  • Materials Informatics

Background:

  • The Crystallography Open Database (COD) is a vital resource for crystallographic data.
  • Ensuring the quality and consistency of data within large databases is crucial for scientific reproducibility.
  • The Crystallographic Information Framework (CIF) provides a standardized format for crystallographic data.

Purpose of the Study:

  • To describe the data curation practices of the Crystallography Open Database (COD).
  • To detail the formal validation of CIF files within the COD using the CIF standard.
  • To present tools and results that aid in data maintenance and ontology development.

Main Methods:

  • Utilized the `cif_validate` program for formal validation of CIF files.
  • Validated the entire Crystallography Open Database (COD) against DDL1 and DDLm dictionaries.
  • Developed programs to assist in the migration from DDL1 to DDLm dictionaries.

Main Results:

  • Processed over 450,000 CIF files from the COD.
  • Validation results provide a valuable resource for data maintenance.
  • Demonstrated the utility of validation in the development of crystallographic ontologies.

Conclusions:

  • Formal validation using CIF is essential for maintaining high-quality crystallographic data.
  • The presented tools facilitate data curation and dictionary migration.
  • Improved data integrity in the COD supports advancements in crystallography and related fields.