Patent Application
20230135352
This invention relates to an electron cryomicroscopy system and a method of operating an electron cryomicroscope.
In less than ten years, electron cryomicroscopy (cryoEM) has become a mainstream technique in structural biology. Today, high-end 300 keV electron microscopes, equipped with high detective quantum efficiency (DQE) direct electron detectors and powerful computing, are routinely being used to determine relatively easily structures that would have been thought impossible just a few years ago (Kühlbrandt, W. (2014) Science, 343, 1443-1444.; Crowther, R. A. (2016). The Resolution Revolution: Recent Advances In CryoEM. Cambridge: Academic Press). Still, electron cryomicroscopes are not optimized for structural biology from the point of view of efficient structure determination or cost. Recent work examined the role of electron energy quantitatively for cryoEM of a biological specimen embedded in vitrified water (Peet, M. J., Henderson, R. & Russo, C. J. (2019) Ultramicroscopy, 203, 125-131). This work showed theory and experiments to determine the optimum electron energy for a biological specimen of a given thickness. The conclusion was that there is a potential improvement of up to 25% in the amount of information available per unit damage for typical single-particle cryoEM specimens which could be realized by reducing the energy of the electron beam from the typical 300 or 200 keV to 100 keV.
Furthermore, the initial expense and running costs of high-end electron microscopes present a significant barrier to the widerspread adoption of cryoEM (Vinothkumar, K. R. & Henderson, R. (2016) Q. Rev. Biophys. 49, e13). A typical high-end instrument has a marginal cost of about £3000 per day to operate (Passmore, L. A. & Russo, C. J. (2016) Methods Enzymol. 579, 51-86), corresponding to a full cost of more than £5000 per day, which is well beyond what most individual laboratories that would potentially benefit from the use of cryoEM could afford.
In its simplest form, an electron cryomicroscope must have a bright electron source, a stable stage, a low ice-contamination rate and a large-area, high-efficiency imaging detector. The first three are available in various commercial instruments, but not together in a single microscope designed for high-resolution 100 keV imaging. Optimized large-area imaging detectors for 100 keV electrons are not currently available from any vendor, thus making the detector the limiting technological factor in establishing cryoEM at 100 keV. The same scattering processes that control electron interaction with the specimen also limit scattering within the electron detector (McMullan, G., Chen, S., Henderson, R. & Faruqi, A. R. (2009) Ultramicroscopy, 109, 1126-1143; Faruqi, A. R. & McMullan, G. (2018) Nucl. Instrum. Methods Phys. Res. A, 878, 180-190). A 300 keV electron has a range of 350 μm in silicon (McMullan, G., Cattermole, D., Chen, S., Henderson, R., Llopart, X., Summerfield, C., Tlustos, L. & Faruqi, A. (2007) Ultramicroscopy, 107, 401-413), and back-thinning a sensor to 30 μm results in most incident electrons being transmitted through the sensor with very little transverse scattering. A pixel size of ˜8 μm can therefore be used to record the arrival position and hence the spatial information contained in the electron beam. The energy deposited in the sensitive layer of the sensor is sufficient to record almost every electron, and the effect of intrinsic variability in the magnitude of the energy deposited is removed by operating in a counting mode (McMullan, G., Chen, S., Henderson, R. & Faruqi, A. R. (2009). Ultramicroscopy, 109, 1126-1143; McMullan, G., Clark, A. T., Turchetta, R. & Faruqi, A. R. (2009) Ultramicroscopy, 109, 1411-1416; Li, X., Mooney, P., Zheng, S., Booth, C. R., Braunfeld, M. B., Gubbens, S., Agard, D. A. & Cheng, Y. (2013). Nat. Methods, 10, 584-590). Monte Carlo simulations of electron trajectories show that 100 keV electrons have a range of 50-60 μm in silicon (McMullan, G., Cattermole, D., Chen, S., Henderson, R., Llopart, X., Summerfield, C., Tlustos, L. & Faruqi, A. (2007) Ultramicroscopy, 107, 401-413). This makes it impractical to back-thin a detector to a thickness at which most of the incident electrons would be transmitted, and also sets a lower bound for the optimal pixel size of 60 μm for a silicon sensitive layer. Detectors optimized for 300 keV electrons can be used at 100 keV by binning their output to give ˜60 μm pixels, but they will have a much smaller field of view, reduced dynamic range and unnecessary computational overhead in the data-output stream.
Hybrid pixel detectors offer an alternative for imaging 100 keV electrons (Faruqi, A. R. & McMullan, G. (2018) Nucl. Instrum. Methods Phys. Res. A, 878, 180-190). Originally designed for particle physics (Heijne et al., (1994) Nucl. Instrum. Methods Phys. Res. A, 348, 399-408), hybrid pixel detectors have recently found wide success in structural biology for photon counting in X-ray detection work (Dinapoli et al., Nucl. Instrum. Methods Phys. Res. A, 650, 79-83; Casanas et al., (2016). Acta Cryst. D 72, 1036-1048). In these detectors, incident electrons strike a thick semiconductor layer that is fully depleted via an applied bias voltage. Energy lost by an incident electron generates charge in the layer that is collected by an array of bump bonds (each comprising a pixel) to a specifically designed readout chip (application-specific integrated circuit; ASIC) containing charge-shaping, thresholding and counting electronics. The bump bonds are typically spaced from 55 to 75 μm apart and define the pitch of the pixel array. As the electronics associated with each bump bond work independently, hybrid pixel detectors can operate at very high speeds (˜10 kHz frame rate). Hybrid pixel detectors have the added advantage of being impervious to high exposure to a 100 keV electron beam, and their application in electron microscopy and crystallography has been explored (Faruqi, A. R., Henderson, R. & Tlustos, L. (2005). Nucl. Instrum. Methods Phys. Res. A, 546, 160-163; Mir et al., (2017) Ultramicroscopy, 182, 44-53; Tinti, G., Fröjdh, E., van Genderen, E., Gruene, T., Schmitt, B., de Winter, D. A., Weckhuysen, B. M. & Abrahams, J. P. (2018). IUCrJ, 5, 190-199). For example, it is possible to switch to and from diffraction mode with no damage to the detector, and to use the same detector for alignment, search and imaging. For application in cryoEM the main limitation is the difficulty in making suitably large (≥2 k×2 k) gapless detectors.
Recent work has also shown that high-resolution cryoEM is possible at 200 keV (Herzik, M. A. Jr, Wu, M. & Lander, G. C. (2017). Nat. Methods, 14, 1075-1078; Herzik, M. A. Jr, Wu, M. & Lander, G. C. (2019). Nat. Commun. 10, 1032).
Reducing the electron energy from the current standard of 300 or 200 keV offers both cost savings and potentially improved imaging. However, currently available electron cryomicroscopes in the 100-120 keV range are not optimized for cryoEM as they lack both the spatially coherent illumination needed for the high defocus used in cryoEM and imaging detectors optimized for 100 keV electrons.
In accordance with a first aspect of the invention, there is provided an electron cryomicroscopy system comprising: a field-emission gun for generating an electron beam, the field-emission gun being energized, in use, to generate a 80 keV to 120 keV electron beam which is emitted into a vacuum enclosure and towards a specimen holder; the vacuum enclosure containing, at least in part: an objective lens for focusing an image of the specimen, the objective lens being disposed in the path of the electron beam and having a chromatic aberration coefficient, Cc, selected to achieve a resolution value better than a desired amount; the specimen holder for holding a specimen, the specimen holder being disposed in the path of the electron beam; a cryostage for cooling a specimen; a cryo-shield for surrounding a specimen and reducing an ice contamination rate of the specimen; and a direct electron detector comprising an array of pixels, each pixel capable of detecting an incident electron that has passed through a sample and struck the pixel.
Keeping the electron beam energy at this range mitigates radiation damage to biological specimens and enhances the information content. It further offers cost saving to a user compared to the current standard of 300 or 200 keV imaging machines.
The resolution value may be better than 2.5 Å.
The cryo-shield may reduce the ice contamination rate of the specimen to below 7 Å per hour.
The system may further comprises one or more processors; and one or more memories operatively coupled to the one or more processors and comprising instructions that when executed by at least one of the one or more processors cause the system to process images of single electron events, based on their pattern and energy distribution at 80 to 120 keV to maximise the detective quantum efficiency (DQE), wherein the images of the single electron events are obtained from the direct electron detector.
The field-emission gun may, preferably, be energized to generate a 90 keV to 110 keV electron beam. Even more preferably, the field-emission gun may be energized to generate a 95 keV to 105 keV electron beam. However, in the most preferred configuration, the field-emission gun is energized to generate a 100 keV electron beam. A 100 keV electron beam has been found to be the optimal value for use with protein structures as it presents the best trade-off between the highest information content, detective quantum efficiency (DQE) and mitigates radiation damage.
In accordance with a second aspect of the invention, there is provided a method of operating an electron cryomicroscope comprising: configuring a field-emission gun of the electron cryomicroscope to generate a 80 keV to 120 keV electron beam; evacuating a vacuum enclosure of the electron cryomicroscope, wherein the electron beam is emitted into the vacuum enclosure and towards a specimen holder of the cryomicroscope; selecting an objective lens for focusing an image of a specimen, the objective lens having an aberration coefficient, Cc, selected to achieve a resolution value better than a desired amount; disposing the objective lens in the path of the electron beam; introducing a specimen to the specimen holder; operating a cryostage for cooling the specimen; selecting a cryo-shield for surrounding a specimen and reducing an ice contamination rate of the specimen; and using a direct electron detector to detect an incident electron that has passed through a sample.
The method may further comprise selecting an objective lens to achieve a resolution value better than 2.5 Å.
The method may further comprises selecting a cryo-shield to achieve an ice contamination rate of the specimen to below 7 Å per hour.
The method may further comprises processing images of single electron events obtained from the detector, the processing of the images based on their pattern and energy distribution at 80 to 120 keV to maximise the detective quantum efficiency (DQE).
The field-emission gun may, preferably, be configured to generate a 90 keV to 110 keV electron beam. Even more preferably, the field-emission gun may be configured to generate a 95 keV to 105 keV electron beam. However, in the most preferred configuration, the field-emission gun is configured to generate a 100 keV electron beam, 100 keV being the optimal value for use with protein structures as it presents the best trade-off between information content per unit of radiation damage and beam attrition due to increased scattering cross-section.
The method may further comprise providing a specimen in the specimen holder. The thickness of the specimen is preferably based on the thickness of ice required for typical protein dimensions and the information content per unit of damage and beam attrition. The specimen may be encapsulated in a layer of water, which will be frozen in use in the cryostage, with a thickness of 100 to 500 Å. More preferably, the thickness of the water layer may be 200 to 400 Å, with a value of 300 Å being particularly preferred.
A hybrid pixel detector (Dectris EIGER X 500K) was used. It is composed of eight 256×256 pixel modules bump-bonded in a 4×2 array, with a two-pixel spacing between modules, to a 450 μm thick silicon sensor. This corresponds to 1030×514 square 75 μm pixels. The EIGER is designed for X-ray detection; to image electrons it was placed in a vacuum housing with an opening for the beam at the top of the chamber. This was made by the MRC LMB workshop and is shown in
The raw data from the detector were mirrored to a second capture computer with custom software designed to provide a simple interface for low-dose data collection. Charge generated in the gap between modules is collected in neighbouring pixels, so the application of a suitable gain correction (
Escherichia coli DNA protection during starvation protein (DPS; Wolf, S. G., Frenkiel, D., Arad, T., Finkel, S. E., Kolter, R. & Minsky, A. (1999) Nature (London), 400, 83-85; amino acids 2-167) was PCR-amplified and cloned into a pET-15b plasmid by Gibson assembly. The construct was composed of DPS fused to an N-terminal hexahistidine tag and TEV proteolytic site (Ser2 in the P7 site). The expression vector was transformed into E. coli BL21-CodonPlus(DE3)-RIL cells (Stratagene) and selected on ampicillin-containing LB agar. 2×YTAmp medium was inoculated with a single colony and cultured overnight at 37° C. with shaking. TBAmp medium was then inoculated 1:50(v:v) with pre-culture and grown at 25° C. At an OD600 nm of 0.8, DPS expression was induced with 0.1 mM IPTG for 18 h. Cells (˜20 g l−1) were harvested by centrifugation and resuspended 1:1(v:v) in lysis buffer (50 mM Tris-Cl− pH 8.0 at 4° C., 500 mM NaCl). Cell suspensions were either processed immediately or flash-frozen in liquid nitrogen and stored at −80° C.
Cells amounting to 1 l of culture were diluted 1:4(w:v) with lysis buffer supplemented with 2.5 mM MgCl2, 20 μs ml−1 DNase I, 100 μs ml−1 lysozyme and protease-inhibitor cocktail tablets (Roche) and allowed to stir on ice for 30 min. The cells were lysed by sonication for 5 minutes at a 33% duty cycle (3 s on, 6 s off) and clarified by centrifugation at 50 000 g for 20 minutes. The supernatant was passed through a 0.45 μm filter and supplemented with 10 mM imidazole before loading onto a 5 ml HisTrap FF column (GE Healthcare) at 2 ml min−1 at 4° C. The column was washed with 20 column volumes of lysis buffer supplemented with 40 mM imidazole before eluting with five column volumes of buffer containing 500 mM imidazole. The eluate was treated with 5 mg TEV protease (+0.5 mM TCEP) and transferred to 3.5 kDa molecular-weight cutoff (MWCO) Snakeskin dialysis tubing (Thermo Fisher Scientific). Imidazole was removed by dialysis against 20 mM Tris-Cl− pH 7.5 at 20° C., 100 mM NaCl, 0.5 mM TCEP with two changes of buffer. In order to remove any residual DNA-bound DPS, the sample was passed through a 5 ml HiTrap DEAE FF column (GE Healthcare). The flowthrough was supplemented with 10 mM imidazole and subjected to negative chromatography on a 5 ml HisTrap FF column. The final flowthrough was concentrated to ˜1.5 ml using a 10 kDa MWCO Amicon Ultra-15 (Millipore Sigma). Approximately one third of the sample was injected at 0.5 ml min−1 onto a Superdex 200 Increase 10/300 GL column (GE Healthcare) equilibrated in 10 mM HEPES-Na+ pH 7.5, 100 mM NaCl. DPS eluted predominantly as a single major peak with a calibrated retention volume equivalent to 205 kDa or a 5.1 nm Stokes radius and with an estimated purification yield of 30-40 mg DPS per litre of culture. The purified DPS runs as a single band around 20 kDa, corresponding to the monomer of the homododecamer, on Tris-Glycine 4-20% SDS-PAGE (
Single-Particle cryoEM Specimen Preparation
Human haemoglobin (Sigma, catalogue No. H7379) was resuspended in PBS (125 mM NaCl, 8 mM NaH2PO4 pH 7.4) to 7.2 mg ml−1 concentration. Horse (Equus caballus) spleen apoferritin (Sigma, catalogue No. A3660) was buffer-exchanged into PBS at pH 7.4 and adjusted to 12.1 mg ml−1 concentration. This specimen was only used for preliminary detector testing and was not used for high-resolution data collection. Commercially available catalase from human erythrocytes (Sigma, catalogue No. C3556) was used at 2 mg ml−1 concentration as supplied in 50 mM Tris-HCl. DPS, purified as described above, was buffer-exchanged into 20 mM HEPES pH 7.7, 150 mM KCl to a final concentration of 0.6 mg ml−1. Purified hepatitis B virus capsids were provided by Jan Löwe and were adjusted to 9.6 mg ml−1 concentration (in 50 mM Tris-HCl, 150 mM NaCl pH 7.4). E. coli 70S ribosomes were purified by published ultracentrifugation methods (Brown, A., Fernández, I. S., Gordiyenko, Y. & Ramakrishnan, V. (2016) Nature (London), 534, 277-280) and were used at 3.5 mg ml−1 concentration (in 10 mM Tris pH 7.5, 50 mM potassium chloride, 10 mM ammonium chloride, 10 mM magnesium acetate, 6 mM β-mercaptoethanol). All cryo-specimens were prepared on all-gold supports (UltrAuFoil R0.6/1, 300 mesh, Quantifoil) with ˜800 nm hole diameter treated with 9:1 Ar:O2 plasma (in a Fischione 1070 chamber) for 60 s to render them hydrophilic. Specimens were vitrified by plunge-freezing in a 4° C. cold room using a manual plunger of the Talmon type (Bellare, J. R., Davis, H. T., Scriven, L. E. & Talmon, Y. (1988) J. Electron Microsc. Tech. 10, 87-111) and a liquid-ethane cryostat set to −181° C. (Russo, C. J., Scotcher, S. & Kyte, M. (2016). Rev. Sci. Instrum. 87, 114302). A sample volume of 3 μl was pipetted onto the foil side of the grid, the droplet was blotted for 15 s from the same side and the grid was plunged into the liquid ethane. The specimens were stored in liquid nitrogen until imaging.
The coefficients of spherical aberration (Cs) and chromatic aberration (Cc) were measured for the Tecnai F20 electron microscope used, equipped with a TWIN-type objective lens and operated at 100 keV. All micrographs for these measurements were recorded on an Orius phosphor-coupled CCD (Gatan).
A platinum/iridium specimen (Agar S114) was used with an ˜400 Å thick gold film evaporated on half of its grid squares. Firstly, the column was aligned to reduce the beam tilt to less than 0.5 mrad by performing sequential tableaux (Zemlin, F., Weiss, K., Schiske, P., Kunath, W. & Herrmann, K. H. (1978) Ultramicroscopy, 3, 49-60) at around 0.5 μm defocus. The pixel size was accurately calibrated using the reflections from the gold crystals. The amount of beam tilt was calibrated by measuring the shift of the diffraction pattern of the gold when changing the rotation-centre alignments by a constant value. The spherical aberration coefficient was then measured via a Zemlin tableau with 4.8 mrad beam tilt in eight directions using a platinum/iridium specimen (Agar S114). A beam-tilt angle of β causes an apparent CTF overfocus of ΔF=2Cs β2 (McFarlane, S. C. (1975). J. Phys. C. Solid State Phys. 8, 2819-2836). The CTFs were fitted to all patterns from the tableau using Gctf (Zhang, K. (2016). J. Struct. Biol. 193, 1-12). The tableau was repeated three times, and the average value of the fitted defoci for the tilted-beam micrographs was subtracted from the average value of the fitted defoci for the central (near-zero beam tilt) micrograph. The principal limitation to the accuracy of this measurement is the ˜100 Å accuracy of the CTF fits and the ˜0.2 mrad accuracy of the applied beam tilt. Based on this measurement, the Cs can be estimated to be 2.2±0.2 mm. The fitted defocus values depend weakly on the initial Cs value used for the fit; in this case, values between 1 and 2 mm consistently yielded the same (within error) Cs estimate from the tableau. The measured value is in agreement with the value reported (Cs=2 mm) for this microscope at 200 keV. The measured Cs value was used for CTF fitting when processing the cryoEM data.
The chromatic aberration coefficient was extracted from the dependence of the defocus on the accelerating voltage. The accelerating voltage was varied from 98 to 102 kV in 1 kV increments, and micrographs of the same platinum/iridium specimen at the same position were recorded; this was repeated three times. The CTFs were fitted using Gctf, and from these fits one can determine that the defocus increases by 11 Å for every 1 eV increase in the accelerating voltage. This is related to the chromatic aberration Cc by
where Δz is the defocus change for energy change ΔE around a value of E=100 keV, and E0 is the rest energy of the electron (511 keV) (Reimer, L. & Kohl, H. (2008). Transmission Electron Microscopy:Physics of Image Formation, 5th ed. New York: Springer). Based on this measurement, a chromatic aberration Cc of 2.0±0.2 mm was determined. The energy spread from a similar gun design operated under similar conditions (extraction voltage and temperature) at 100 keV on a Polara equipped with a calibrated energy spectrometer shows that the source-energy spread for all of the data collected here was in the range 1.0-1.3 eV. Note that Schottky guns of this type can be operated under conditions of lower spread (ΔE=0.6-0.8 eV). As is evident from the denominator of the equation, even with the same value of Cc the effect of this aberration is approximately three times stronger at 100 kV than at 300 kV.
All data collection was performed on a Tecnai F20 electron microscope operated at 100 kV and fitted with an EIGER X 500K detector [
A gain reference was produced by averaging all frames of all exposures for each data set and was applied to all movies. Defects on the detector were corrected by replacing the pixel values with the average of the adjacent pixels. All movies were motion-corrected using the RELION-3 implementation of motion correction (Zivanov, J., Nakane, T., Forsberg, B. O., Kimanius, D., Hagen, W. J. H., Lindahl, E. & Scheres, S. H. W. (2018). Elife, 7, e42166). The typical stage-drift rate (uniform motion in a single direction) during these exposures was found to be 7 Å s−1.Dose-weighting was applied, as implemented in RELION-3, by scaling the radiation-damage rate assumed at 300 kV by a factor of 1.57, as measured for the inelastic electron scattering cross-section from carbon at 100 kV compared with 300 kV (Peet, M. J., Henderson, R. & Russo, C. J. (2019). Ultramicroscopy, 203, 125-131). Power spectra were calculated for groups of every three frames. CTFs were fitted to these power spectra in the 25-4 Å resolution range using CTFFIND 4.1 (Rohou, A. & Grigorieff, N. (2015). J. Struct. Biol. 192, 216-221) with amplitude contrast 0.07 (Toyoshima, C. & Unwin, N. (1988). Ultramicroscopy, 25, 279-291) and spherical aberration 2.0 mm (
For the DPS data set, 68 817 particles were manually picked from 739 micrographs [
For the haemoglobin data set, 64 986 particles were manually picked from 576 micrographs [
For the catalase data set, 11 948 particles were manually picked from 133 micrographs [
For the 70S ribosome data set, 7560 particles were manually picked from 127 micrographs [
For the hepatitis B virus capsid data set, 167 particles were manually picked from 23 micrographs [
The efficiency of all resulting orientation distributions was estimated using cryoEF (Naydenova, K. & Russo, C. J. (2017). Nat. Commun. 8, 629). All orientation distributions in
The structures of five biological specimens were determined, hepatitis B virus capsid, E. coli 70S ribosome, catalase, haemoglobin and DPS, in seven days of data collection at 100 kV using the EIGER X 500K detector. Replacing the detector on the microscope took one day, as did reverting the microscope to its original configuration at the end of these experiments. During the data collection, 97% of the pixels on the detector were usable. A four-pixel-wide rim around the edge of the detector and an 8×256 pixel stripe across the field of view were not usable, with constant high-number readout. In addition to the defective stripes, four pixels at each of the eight locations of the ASIC boundaries around the edge had a fixed output. All these defective pixels were replaced with the average value of the neighbouring pixels after gain correction.
The highest resolution structure determined was that of the 220 kDa protein DPS with tetrahedral symmetry, which reached 3.4 Å resolution from 16 500 particles. At this resolution, the density for most side chains is sufficiently clear to allow model building. From the 2D class averages, the twofold and threefold symmetric views can be distinguished. To obtain 2D classes with clear secondary-structure features, the CTF values up to the first peak, owing to the strong form-factor signal of the particles, were ignored [
The structure of catalase from human erythrocytes (240 kDa, D2 symmetry) was determined nominally to 6.5 Å resolution, calculated by the gold-standard FSC at 0.143 (Harauz, G. & van Heel, M. (1986). Optik, 73, 146-156; Rosenthal, P. B. & Henderson, R. (2003). J. Mol. Biol. 333, 721-745; Scheres, S. H. W. & Chen, S. (2012). Nat. Methods, 9, 853-854). The actual resolution of the map is strongly anisotropic, ranging from better than 4 Å in the plane of the preferred view to 10 Å in the orthogonal direction, owing to the preferred orientation exhibited by this protein, i.e. the low efficiency (E=0.2) of the orientation distribution [
The larger specimens ribosomes (
It can be demonstrated that one can also image specimens at the lowest size limit of cryoEM. The structure of haemoglobin (64 kDa, with C2 symmetry) can be determined to 8.4 Å resolution, where clear α-helix separation can be observed. At this resolution one could distinguish, for example, the conformational difference between oxyhaemoglobin and deoxyhaemoglobin.
The microscope, as configured for this study, is capable of resolving a 3.4 Å lattice in all directions at 100 keV on a standard test specimen such as graphitized carbon without the use of tilt and the 2.35 Å gold lattice. Since the spherical aberration of the lens is corrected for accurately during the reconstruction process, it should not pose any limitations to high-resolution imaging of biological specimens at 100 keV. In contrast, the effect of chromatic aberration increases at lower accelerating voltages owing to the increase in the fractional energy spread ΔE/E and the increase in the electron wavelength λ. Comparing electron beams with the same energy spread ΔE, the envelope function Kc(q) that damps the CTF oscillations at spatial frequency q is
which decays to lie at an approximately 2.2× lower spatial frequency at 100 kV than at 300 kV (Reimer, L. & Kohl, H. (2008). Transmission Electron Microscopy:Physics of Image Formation, 5th ed. New York: Springer). Similarly, the phase errors owing to beam tilt become more pronounced at 100 keV than at 300 keV owing to the longer wavelength of the electrons; these can be corrected for in the software as well, as shown in the example of the DPS data set.
A 100 keV electron microscope equipped with a field-emission gun (FEG) and a direct electron detector is suitable for imaging vitrified biological specimens at high resolution. Such an instrument is especially useful for screening specimens for suitable ice thickness, protein quality and orientation distribution efficiency. All the reconstructions reported here achieved sufficient resolution to provide useful information about the specimen orientation in the micrographs; the same strategy of quick reconstructions from small data sets can be used, for example, to optimize the choice of specimen supports and grid-freezing conditions for high-resolution data collection. Specimen evaluation and optimization could be greatly accelerated if inexpensive 100 kV instruments with a FEG source and a direct detector were readily available. With the example of DPS, it was demonstrated that a 3.4 Å resolution structure can be determined using such an instrument.
The current technical limitation to high-resolution imaging at 100 keV is the small detector area. The micrographs shown in
Affordable cryoEM
It is possible to determine subnanometre structures of a variety of vitrified biological specimens by cryoEM using 100 keV electrons. The following is a list of the key requirements for an affordable electron cryomicroscope.
(i) High vacuum (<10−7 Torr) with a good anti-ice cryoshield surrounding the specimen (Homo, J.-C., Booy, F., Labouesse, P., Lepault, J. & Dubochet, J. (1984). J. Microsc. 136, 337-340). It is easy to show that at 10−6 Torr there would be 1015 water molecules per cm2 (a monolayer) per second striking all surfaces in the vacuum, and a tenth of a monolayer per second at 10−7 Torr. An ice-contamination rate of less than 7 Å per hour would allow the careful examination of single cryoEM grids while retaining the option of continuing data collection for a period of up to 8 h. A cryostage with a reduced drift rate (<1 Å during a typical exposure) would facilitate high-resolution data collection.
(ii) It is essential to have a field-emission gun (FEG) source (Schottky or cold) to provide sufficient spatial coherence to take 1-2 s exposures that allow the use of enough defocus to give low-resolution contrast while retaining high-resolution detail (Russo, C. J. & Henderson, R. (2018b). Ultramicroscopy, 187, 56-63; Börrnert, F., Renner, J. & Kaiser, U. (2018). Microsc. Microanal. 24, 249-255).
(iii) A small chromatic aberration coefficient, Cc, for the objective lens is a more stringent requirement at 100 keV than at 300 keV (equations 1 and 2), if the resolution requirement of the microscope needs to include the ability to reach a resolution beyond 3 Å, which may be useful for some projects. For a source with energy spread ΔE≲5.1 eV, a Cc of less than 2 mm would be adequate, which is available on existing microscopes. This places a restriction on the pole gap and bore, but can easily be accommodated provided that large specimen tilts are not required. A tilt range of ±10° would be useful for single-particle cryoEM, but electron tomography would not be possible with 3 mm foils.
(iv) As shown here, the most urgent need is for the development of a large-area direct electron detector that is optimized to give a high DQE at 100 keV. At present, phosphor/fibre-optics cameras work reasonably well but have DQEs that are too low for effective cryoEM. The Dectris EIGER X 500K detector used in this paper has excellent performance, but the active area is too small for convenient and efficient use. A purpose-designed detector (CMOS or hybrid pixel) with a square area of 2000 or 3000 pixels on edge would be ideal, 8× to 16× larger than the detector used in this paper. The main constraint for recording high-DQE images at 100 keV arises from the greatly increased electron scatter in the detector, for which the simplest solution is to develop a design that uses a larger pixel whose size matches the range of electron scattering in the detector.
(v) To reach a DQE(0) that is near 100%, every electron that deposits energy in the detector should be counted individually (Turchetta, R. (1993). Nucl. Instrum. Methods Phys. Res. A, 335, 44-58; Li et al., (2013). Nat. Methods, 10, 584-590; McMullan, G., Faruqi, A. R., Clare, D. & Henderson, R. (2014). Ultramicroscopy, 147, 156-163). With improvements to the data-acquisition system (DAQ) the current detector would have an almost perfect DQE: better than 0.99 at zero spatial frequency and better than 0.6 at the Nyquist frequency. The same constraints apply to the DAQs for both monolithic active pixel sensors using CMOS technology and to hybrid pixel sensors such as the EIGER used here.
(vi) For wide adoption, an affordable electron cryomicroscope should be easy to use and have modest requirements from the laboratory in which it is housed. This includes relative insensitivity to electric and magnetic fields, vibrations and temperature fluctuations. The physical size, installation and maintenance requirements should also be moderate, such that most laboratory spaces would be suitable. Reducing the accelerating voltage to 100 kV and targeting a resolution of 3 Å makes this easier to accomplish.
Ultimate cryoEM
Finally, one can consider what would be required to create a 100 keV electron microscope that could routinely achieve better than 2 Å resolution on biological specimens.
Previous work on radiation-hard specimens such as graphene have shown that <1 Å resolution is possible at 80 keV (Bell, D. C., Russo, C. J. & Benner, G. (2010). Microsc. Microanal. 16, 386-392), 40 keV (Bell, D. C., Russo, C. J. & Kolmykov, D. V. (2012). Ultramicroscopy, 114, 31-37) and even 20 keV (Linck et al., (2016). Phys. Rev. Lett. 117, 076101; Börrnert, F. & Kaiser, U. (2018). Phys. Rev. A, 98, 023861). It is clear from this work and from other recent results using post-data-collection aberration correction in software (Zivanov, J., Nakane, T., Forsberg, B. O., Kimanius, D., Hagen, W. J. H., Lindahl, E. & Scheres, S. H. W. (2018). Elife, 7, e42166) that the limiting factor is the chromatic aberration of the lens. There are several ways to mitigate the effects of Cc, as is evident from (1). The first and simplest is to reduce the extraction voltage and temperature of a Schottky-type FEG to their minimum, thus reducing the energy spread to around 0.7-0.5 eV. Secondly, one can use a cold FEG, which reduces the energy spread of the source even further but requires better vacuum and periodic flashing to refresh the integrity of the tip. Thirdly, one can employ the use of a monochromator to reduce the energy spread of either type of source to <100 meV. This has been shown to increase the bounds of the envelope function and improve the resolution of a Schottky-type source to 1 Å (Bell, D. C., Russo, C. J. & Benner, G. (2010). Microsc. Microanal. 16, 386-392; Mukai et al., (2014). Ultramicroscopy, 140, 37-43). Fourthly, an objective lens design can be optimized for minimal Cc at the expense of other parameters such as the gap distance. Finally, a full hardware Cc corrector can be added to reduce the Cc of the image-forming lens to an arbitrarily low value and thus eliminate this part of the envelope function entirely (Rose, H. H. (2009). Philos. Trans. R. Soc. A, 367, 3809-3823; Zach, J. (2009). Philos. Trans. R. Soc. A, 367, 3699-3707; Kabius, B., Hartel, P., Haider, M., Muller, H., Uhlemann, S., Loebau, U., Zach, J. & Rose, H. (2009). J. Electron Microsc. 58, 147-155; Haider, M., Hartel, P., Müller, H., Uhlemann, S. & Zach, J. (2010). Microsc. Microanal. 16, 393-408). It can be envisioned that future cryomicroscopes designed for ultimate resolution in single-particle work will be designed both to maximize the information coefficient (information available per unit damage; Peet, M. J., Henderson, R. & Russo, C. J. (2019). Ultramicroscopy, 203, 125-131) and minimize the presence or effects of Cc along with other geometric aberrations of the objective lens as necessary. In some instruments this may involve the use of a monochromator (Krivanek et al., (2009). Philos. Trans. R. Soc. A, 367, 3683-3697; Essers, E., Benner, G., Mandler, T., Meyer, S., Mittmann, D., Schnell, M. & Hoschen, R. (2010). Ultramicroscopy, 110, 971-980; Tsuno, K. (2011). Nucl. Instrum. Methods Phys. Res. A, 645, 12-19) or a cold FEG (Crewe, A. V., Eggenberger, D. N., Wall, J. & Welter, L. M. (1968). Rev. Sci. Instrum. 39, 576-583) to reduce the energy spread of the source with a small gap lens, or in the case of high-end instruments a Cc corrector to reduce the Cc to negligible values (Forbes, B. D., Houben, L., Mayer, J., Dunin-Borkowski, R. E. & Allen, L. J. (2014). Ultramicroscopy, 147, 98-105; Linck et al., (2016). Phys. Rev.Lett. 117, 076101). This will then allow true atomic resolution (˜1 Å) cryoEM on appropriate specimens where the additional cost and effort required to achieve these resolutions is deemed appropriate and necessary to solve the biological problem of interest.
The subnanometre single-particle cryoEM structures described in this paper provide a practical demonstration that high-quality cryoEM can be performed at 100 keV with relatively unsophisticated equipment. Currently, the lack of a suitable high-speed, high-efficiency detector with a large number of pixels (>4×106) is the primary limitation both to the ultimate achievable resolution and to the practical use of a 100 keV transmission electron microscope for cryoEM. With additional investment in the development of improved 100 keV detectors and field-emission sources, the use of cryoEM in structural biology could be greatly expanded. Further, a path to creating a fully optimized, atomic resolution electron cryomicroscope, which can rapidly determine the structures of single-particle specimens, is now clear.
| Number | Date | Country | Kind |
|---|---|---|---|
| 1914695.0 | Oct 2019 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2020/078515 | 10/9/2020 | WO |
