X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the positions of the atoms in the crystal can be determined, as well as their chemical bonds, crystallographic disorder, and various other information.
Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM). It can involve the use of high-resolution transmission electron microscopy images, electron diffraction patterns including convergent-beam electron diffraction or combinations of these. It has been successful in determining some bulk structures, and also surface structures. Two related methods are low-energy electron diffraction which has solved the structure of many surfaces, and reflection high-energy electron diffraction which is used to monitor surfaces often during growth.
Crystallographic Information File (CIF) is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography (IUCr). CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. The file format was initially published by Hall, Allen, and Brown and has since been revised, most recently versions 1.1 and 2.0. Full specifications for the format are available at the IUCr website. Many computer programs for molecular viewing are compatible with this format, including Jmol.
In X-ray crystallography, a difference density map or Fo–Fc map shows the spatial distribution of the difference between the measured electron density of the crystal and the electron density explained by the current model.
Multi-wavelength anomalous diffraction is a technique used in X-ray crystallography that facilitates the determination of the three-dimensional structure of biological macromolecules via solution of the phase problem.
Jane Shelby Richardson is an American biophysicist best known for developing the Richardson diagram, or ribbon diagram, a method of representing the 3D structure of proteins. Ribbon diagrams have become a standard representation of protein structures that has facilitated further investigation of protein structure and function globally. With interests in astronomy, math, physics, botany, and philosophy, Richardson took an unconventional route to establishing a science career. Today Richardson is a professor in biochemistry at Duke University.
Axel T. Brunger is a German American biophysicist. He is Professor of Molecular and Cellular Physiology at Stanford University, and a Howard Hughes Medical Institute Investigator. He served as the Chair of the Department of Molecular and Cellular Physiology (2013–2017).
Acta Crystallographica is a series of peer-reviewed scientific journals, with articles centred on crystallography, published by the International Union of Crystallography (IUCr). Originally established in 1948 as a single journal called Acta Crystallographica, there are now six independent Acta Crystallographica titles:
Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and led the Protein Structure Initiative Structural Genomics Knowledgebase.
A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal.
Mamannamana Vijayan was an Indian structural biologist.
Gerard Jacob Kleywegt is a Dutch X-ray crystallographer and the former team leader of the Protein Data Bank in Europe at the EBI; a member of the Worldwide Protein Data Bank.
Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.
Michael Joseph Ezra Sternberg is a professor at Imperial College London, where he is director of the Centre for Integrative Systems Biology and Bioinformatics and Head of the Structural bioinformatics Group.
The Disordered Structure Refinement program (DSR), written by Daniel Kratzert, is designed to simplify the modeling of molecular disorder in crystal structures using SHELXL by George M. Sheldrick. It has a database of approximately 120 standard solvent molecules and molecular moieties. These can be inserted into the crystal structure with little effort, while at the same time chemically meaningful binding and angular restraints are set. DSR was developed because the previous description of disorder in crystal structures with SHELXL was very lengthy and error-prone. Instead of editing large text files manually and defining restraints manually, this process is automated with DSR.
The Multipole Density Formalism is an X-ray crystallography method of electron density modelling proposed by Niels K. Hansen and Philip Coppens in 1978. Unlike the commonly used Independent Atom Model, the Hansen-Coppens Formalism presents an aspherical approach, allowing one to model the electron distribution around a nucleus separately in different directions and therefore describe numerous chemical features of a molecule inside the unit cell of an examined crystal in detail.
Microcrystal electron diffraction, or MicroED, is a CryoEM method that was developed by the Gonen laboratory in late 2013 at the Janelia Research Campus of the Howard Hughes Medical Institute. MicroED is a form of electron crystallography where thin 3D crystals are used for structure determination by electron diffraction. Prior to this demonstration, macromolecular (protein) electron crystallography was only used on 2D crystals, for example.
Durward William John Cruickshank, often known as D. W. J. Cruickshank, was a British crystallographer whose work transformed the precision of determining molecular structures from X-ray crystal structure analysis. He developed the theoretical framework for anisotropic displacement parameters, also known as the thermal ellipsoid, for crystal structure determination in a series of papers published in 1956 in Acta Crystallographica.
Władysław Minor also known as Wladek Minor is a Polish-American biophysicist, a specialist in structural biology and protein crystallography. He is a Harrison Distinguished Professor of Molecular Physiology and Biological Physics at the University of Virginia. Minor is a co-author of HKL2000/HKL3000 – crystallographic data processing and structure solution software used to process data and solve structures of macromolecules, as well as small molecules. He is a co-founder of HKL Research, a company that distributes the software. He is also a co-author of a public repository of diffraction images (proteindiffraction.org) for some of the protein structures available in the Protein Data Bank and other software tools for structural biology.
Urea can crystallise with other compounds. These can be called urea adducts or if a solvent is involved, a urea solvate. Urea can also be a neutral ligand if it is coordinated to a central metal atom. Urea can form hydrogen bonds to other oxygen and nitrogen atoms in the substance it crystallises with. This stiffens the solid and raises the melting point. T
