Potassium channels selectively conduct K + ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K + concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K + ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K + conduction. Crystallographic data are consistent with directly neighboring K + ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K + channels.
15 November 2018 in Angewandte Chemie International Edition
Chemists of all fields currently publish about 50 000 crystal structures per year, the vast majority of which are X‐ray structures. We determined two molecular structures by employing electron rather than X‐ray diffraction. For this purpose, an EIGER hybrid pixel detector was fitted to a transmission electron microscope, yielding an electron diffractometer. The structure of a new methylene blue derivative was determined at 0.9 Å resolution from a crystal smaller than 1×2 μm2. Several thousand active pharmaceutical ingredients (APIs) are only available as submicrocrystalline powders. To illustrate the potential of electron crystallography for the pharmaceutical industry, we also determined the structure of an API from its pill. We demonstrate that electron crystallography complements X‐ray crystallography and is the technique of choice for all unsolved cases in which submicrometer‐sized crystals were the limiting factor.
7 December 2013 in Journal of Applied Crystallography
Some of the improvements inSHELX2013makeSHELXLconvenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to useSHELXLfor refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst.(1991), A47, 392–400] restraints to H atoms and discusses several of the features ofSHELXLthat make the program particularly useful for the investigation of H atoms with neutron diffraction.SHELXL2013is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.
5 February 2016 in Acta Crystallographica Section A Foundations and Advances
Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enablingab initiophasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS,SHELX) and for electron crystallography (ADT3D/PETS,SIR2014).
30 May 2018 in Acta Crystallographica Section D Structural Biology
Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method of data collection has been adapted for the electron microscope. However, there are important differences in geometry that must be considered for successful data integration. The wavelength of electrons in a TEM is typically around 40 times shorter than that of X-rays, implying a nearly flat Ewald sphere, and consequently low diffraction angles and a high effective sample-to-detector distance. Nevertheless, theDIALSsoftware package can, with specific adaptations, successfully process continuous-rotation electron diffraction data. Pathologies encountered specifically in electron diffraction make data integration more challenging. Errors can arise from instrumentation, such as beam drift or distorted diffraction patterns from lens imperfections. The diffraction geometry brings additional challenges such as strong correlation between lattice parameters and detector distance. These issues are compounded if calibration is incomplete, leading to uncertainty in experimental geometry, such as the effective detector distance and the rotation rate or direction. Dynamic scattering, absorption, radiation damage and incomplete wedges of data are additional factors that complicate data processing. Here, recent features ofDIALSas adapted to electron diffraction processing are shown, including diagnostics for problematic diffraction geometry refinement, refinement of a smoothly varying beam model and corrections for distorted diffraction images. These novel features, combined with the existing tools inDIALS, make data integration and refinement feasible for electron crystallography, even in difficult cases.
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.