Crystallographic extraction and averaging of data from small image areas

A Refined Single-Particle Reconstruction Procedure to Process Two-Dimensional Crystal Images from Transmission Electron Microscopy

Single-particle reconstruction (SPR) and electron crystallography (EC), two major applications in electron microscopy, can be used to determine the structure of membrane proteins. The three-dimensional (3D) map is obtained from separated particles in conventional SPR, but from periodic unit cells in EC. Here, we report a refined SPR procedure for processing 2D crystal images. The method is applied to 2D crystals of melibiose permease, a secondary transporter in Escherichia coli. The current procedure is improved from our previously published one in several aspects. The "gold standard Fourier shell correlation" resolution of our final reconstruction reaches 13 Å, which is significantly better than the previously obtained 17 Å resolution. The choices of different refinement parameters for reconstruction are discussed. Our refined SPR procedure could be applied to determine the structure of other membrane proteins in small or locally distorted 2D crystals, which are not ideal for EC.

An alternative model for photosystem II/light harvesting complex II in grana membranes based on cryo-electron microscopy studies

The photosynthetic protein complexes in plants are located in the chloroplast thylakoid membranes. These membranes have an ultrastructure that consists of tightly stacked 'grana' regions interconnected by unstacked membrane regions. The structure of isolated grana membranes has been studied here by cryo-electron microscopy. The data reveals an unusual arrangement of the photosynthetic protein complexes, staggered over two tightly stacked planes. Chaotrope treatment of the paired grana membranes has allowed the separation and isolation of two biochemically distinct membrane fractions. These data have led us to an alternative model of the ultrastructure of the grana where segregation exists within the grana itself. This arrangement would change the existing view of plant photosynthesis, and suggests potential links between cyanobacterial and plant photosystem II light harvesting systems.

Ins and outs of digital electron microscopy

In order to do any sort of computer processing of the images produced by an electron microscope they have to be digitized. Therefore, any form of microscopy that involves computer processing has to be considered as digital microscopy independently of whether the original images were recorded on film and scanned or recorded directly on a digital medium such as the charge coupled device (CCD). As soon as one digitizes images, one encounters a range of effects and artefacts specific to the digital world such as aliasing, quantization errors, and ambiguities in the modulation transfer function. Even a quick discussion of these effects makes it clear that what comes out of a digitizer is not related in a simple way to what goes in. After introducing the commonly used recording media, I will discuss the most important effects of digitization and then compare the limitations and advantages of the different recording media for various applications.

Solution x-ray scattering-based estimation of electron cryomicroscopy imaging parameters for reconstruction of virus particles

Structure factor amplitudes and phases can be computed directly from electron cryomicroscopy images. Inherent aberrations of the electromagnetic lenses and other instrumental factors affect the structure factors, however, resulting in decreased accuracy in the determined three-dimensional reconstruction. In contrast, solution x-ray scattering provides absolute and accurate measurement of spherically averaged structure factor amplitudes of particles in solution but does not provide information on the phases. In the present study, we explore the merits of using solution x-ray scattering data to estimate the imaging parameters necessary to make corrections to the structure factor amplitudes derived from electron cryomicroscopic images of icosahedral virus particles. Using 400-kV spot-scan images of the bacteriophage P22 procapsid, we have calculated an amplitude contrast of 8.0 +/- 5.2%. The amplitude decay parameter has been estimated to be 523 +/- 188 A2 with image noise compensation and 44 +/- 66 A2 without it. These results can also be used to estimate the minimum number of virus particles needed for reconstruction at different resolutions.

Performance of a 2k CCD camera designed for electron crystallography at 400 kV

We discuss the performance of a charge-coupled device (CCD) camera that has been designed for use in electron crystallographic studies of proteins. There have been many previous publications describing the characteristics and performance of CCD-based cameras in electron microscopy; here we focus on characteristics relevant to protein studies at 400 kV. The low exposure that must be used in such studies produces a very poor signal-to-noise ratio, so any loss of signal-to-noise ratio in the recording process must be avoided. Images must contain a sufficient number of molecules to allow identification of the reciprocal lattice, thus requiring a large image format. Electron diffraction patterns may contain some spots with intensity around 10(-7) times that of the central beam, so the largest possible dynamic range is helpful. Some of the characteristics we discuss are most easily measured with crystals, but the conclusions also apply for other work such as single-particle analyses. The camera has been optimized for work at 400 kV with a P43 scintillator fiber-optically coupled to a CCD with 24 microns pixels. The scintillator in this camera is thicker than generally used at lower voltages, which provides an adequate signal level but slightly degrades the resolution. Operation at 400 kV leads to a point spread function that is broader than the CCD pixel size. Images are thus binned by a factor of two to double the effective pixel size, with the resulting loss of a factor of two in the size of areas that can be recorded in a single frame. A large CCD with a 2048 x 2048 pixel array is used to compensate for this loss and provide a sufficient signal for the crystallographic image processing used in this work. Images and electron diffraction patterns recorded on the CCD are compared with data recorded on photographic film. While the quality of the images recorded on the CCD at the low exposures required in protein studies is not quite as good as that on film, electron diffraction data recorded on the CCD are superior to that on film.