Single-particle cryo-EM at atomic resolution.

The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insights into protein function may be inferred. Electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years1,2. However, it has proved difficult to obtain cryo-EM reconstructions with sufficient resolution to visualize individual atoms in proteins. Here we use a new electron source, energy filter and camera to obtain a 1.7 Å resolution cryo-EM reconstruction for a human membrane protein, the ß3 GABAA receptor homopentamer3. Such maps allow a detailed understanding of small-molecule coordination, visualization of solvent molecules and alternative conformations for multiple amino acids, and unambiguous building of ordered acidic side chains and glycans. Applied to mouse apoferritin, our strategy led to a 1.22 Å resolution reconstruction that offers a genuine atomic-resolution view of a protein molecule using single-particle cryo-EM. Moreover, the scattering potential from many hydrogen atoms can be visualized in difference maps, allowing a direct analysis of hydrogen-bonding networks. Our technological advances, combined with further approaches to accelerate data acquisition and improve sample quality, provide a route towards routine application of cryo-EM in high-throughput screening of small molecule modulators and structure-based drug discovery.

Automatic Alignment of an Orbital Angular Momentum Sorter in a Transmission Electron Microscope Using a Convolutional Neural Network.

We report on the automatic alignment of a transmission electron microscope equipped with an orbital angular momentum sorter using a convolutional neural network. The neural network is able to control all relevant parameters of both the electron-optical setup of the microscope and the external voltage source of the sorter without input from the user. It can compensate for mechanical and optical misalignments of the sorter, in order to optimize its spectral resolution. The alignment is completed over a few frames and can be kept stable by making use of the fast fitting time of the neural network.

Experimental Demonstration of an Electrostatic Orbital Angular Momentum Sorter for Electron Beams.

The component of orbital angular momentum (OAM) in the propagation direction is one of the fundamental quantities of an electron wave function that describes its rotational symmetry and spatial chirality. Here, we demonstrate experimentally an electrostatic sorter that can be used to analyze the OAM states of electron beams in a transmission electron microscope. The device achieves postselection or sorting of OAM states after electron-material interactions, thereby allowing the study of new material properties such as the magnetic states of atoms. The required electron-optical configuration is achieved by using microelectromechanical systems technology and focused ion beam milling to control the electron phase electrostatically with a lateral resolution of 50 nm. An OAM resolution of 1.5ℏ is realized in tests on controlled electron vortex beams, with the perspective of reaching an optimal OAM resolution of 1ℏ in the near future.

Towards a holographic approach to spherical aberration correction in scanning transmission electron microscopy.

Recent progress in phase modulation using nanofabricated electron holograms has demonstrated how the phase of an electron beam can be controlled. In this paper, we apply this concept to the correction of spherical aberration in a scanning transmission electron microscope and demonstrate an improvement in spatial resolution. Such a holographic approach to spherical aberration correction is advantageous for its simplicity and cost-effectiveness.

Near-real-time diagnosis of electron optical phase aberrations in scanning transmission electron microscopy using an artificial neural network.

The key to optimizing spatial resolution in a state-of-the-art scanning transmission electron microscope is the ability to measure and correct for electron optical aberrations of the probe-forming lenses precisely. Several diagnostic methods for aberration measurement and correction have been proposed, albeit often at the cost of relatively long acquisition times. Here, we illustrate how artificial intelligence can be used to provide near-real-time diagnosis of aberrations from individual Ronchigrams. The demonstrated speed of aberration measurement is important because microscope conditions can change rapidly. It is also important for the operation of MEMS-based hardware correction elements, which have less intrinsic stability than conventional electromagnetic lenses.

Precise beam-tilt alignment and collimation are required to minimize the phase error associated with coma in high-resolution cryo-EM.

Electron microscopy at a resolution of 0.4nm or better requires more careful adjustment of the illumination than is the case at a resolution of 0.8nm. The use of current-axis alignment is not always sufficient, for example, to avoid the introduction of large phase errors, at higher resolution, due to axial coma. In addition, one must also ensure that off-axis coma does not corrupt the data quality at the higher resolution. We particularly emphasize that the standard CTF correction does not account for the phase error associated with coma. We explain the cause of both axial coma and the typically most troublesome component of off-axis coma in terms of the well-known shift of the electron diffraction pattern relative to the optical axis that occurs when the illumination is not parallel to the axis. We review the experimental conditions under which coma causes unacceptably large phase errors, and we discuss steps that can be taken when setting up the conditions of illumination, so as to ensure that neither axial nor off-axis coma is a problem.

Flexible formation of coherent probes on an aberration-corrected STEM with three condensers.

We have used geometric optics calculations and experiments to investigate the probe-forming capability of an aberration-corrected, three-condenser scanning transmission electron microscope (STEM). Large, minimally convergent and coherent electron probes are useful for a variety of electron diffraction measurements. A three-condenser lens STEM can form a probe either using a virtual aperture below the sample and a virtual source on the sample plane or using a virtual aperture on the sample and a virtual source in the front focal plane. Adding a hexapole probe aberration corrector greatly increases the range of aperture demagnification and thus probe size and convergence angle. We have created probes 0.1 to approximately 12 nm in diameter in the simplest operating mode of our STEM, and we calculate that probes as large as 5000 nm that are almost perfectly parallel may be possible in more exotic lens configurations. We have also measured the spatial coherence of some of these probes.

Atom size electron vortex beams with selectable orbital angular momentum.

The decreasing size of modern functional magnetic materials and devices cause a steadily increasing demand for high resolution quantitative magnetic characterization. Transmission electron microscopy (TEM) based measurements of the electron energy-loss magnetic chiral dichroism (EMCD) may serve as the needed experimental tool. To this end, we present a reliable and robust electron-optical setup that generates and controls user-selectable single state electron vortex beams with defined orbital angular momenta. Our set-up is based on a standard high-resolution scanning TEM with probe aberration corrector, to which we added a vortex generating fork aperture and a miniaturized aperture for vortex selection. We demonstrate that atom size probes can be formed from these electron vortices and that they can be used for atomic resolution structural and spectroscopic imaging - both of which are prerequisites for future atomic EMCD investigations.

Domain (grain) boundaries and evidence of "twinlike" structures in chemically vapor deposited grown graphene.

Understanding and engineering the domain boundaries in chemically vapor deposited monolayer graphene will be critical for improving its properties. In this study, a combination of transmission electron microscopy (TEM) techniques including selected area electron diffraction, high resolution transmission electron microscopy (HR-TEM), and dark field (DF) TEM was used to study the boundary orientation angle distribution and the nature of the carbon bonds at the domain boundaries. This report provides an important first step toward a fundamental understanding of these domain boundaries. The results show that, for the graphene grown in this study, the 46 measured misorientation angles are all between 11° and 30° (with the exception of one at 7°). HR-TEM images show the presence of adsorbates in almost all of the boundary areas. When a boundary was imaged, defects were seen (dangling bonds) at the boundaries that likely contribute to adsorbates binding at these boundaries. DF-TEM images also showed the presence of a "twinlike" boundary.

Atomic scale analysis of planar defects in polycrystalline diamond.

Planar defects in a polycrystalline diamond film were studied by high-resolution transmission electron microscopy (HRTEM) and high-resolution scanning transmission electron microscopy (STEM). In both modes, sub-Angstrom resolution was achieved by making use of two aberration-corrected systems; a TEM and a STEM C(s)-corrected microscope, each operated at 300 kV. For the first time, diamond in (110) zone-axis orientation was imaged in STEM mode at a resolution that allows for resolving the atomic dumbbells of carbon at a projected interatomic distance of 89 pm. Twin boundaries that show approximately the sigma3 CSL structure reveal at sub-Angstrom resolution imperfections; that is, local distortions, which break the symmetry of the ideal sigma3 type twin boundary, are likely present. In addition to these imperfect twin boundaries, voids on the atomic level were observed. It is proposed that both local distortions and small voids enhance the mechanical toughness of the film by locally increasing the critical stress intensity factor.