Identification of grown-in dislocations in protein crystals by digital X-ray topography

Abstract

X-ray topography is a useful and nondestructive method for direct observation of crystal defects in nearly perfect single crystals. The grown-in dislocations from the cross-linked seed crystal in tetragonal hen egg-white lysozyme crystals were successfully characterized by digital X-ray topography. Digital X-ray topographs with various reflections were easily obtained by reconstruction of sequential rocking-curve images. The Burgers vector of the dislocation is different from those reported previously. Interestingly, one of the dislocations had a bent shape. The preferred direction of the dislocation line was analysed by the estimated dislocation energy based on the dislocation theory. The dislocation energy can be estimated by the dislocation theory even in protein crystals composed of macromolecules.

Existence of twisting in dislocation-free protein single crystals

“…The perpendicular shift can be explained by the bending of the crystal along the [001] direction. However, the appearance of the diffraction band and its shift constitute a common behavior caused by beam divergence due to a discrepancy in d -spacing between the sample crystal and monochromator crystal in X-ray diffraction experiments ( 25 , 26 ). The d -spacing of sample tetragonal HEWL (004) is d = 0.948 nm, which is much larger than d = 0.314 nm of the double-crystal monochromator consisting of Si (111) crystals in this experiment.…”

“…2 B – D shows the image obtained by digital X-ray topography, the profiles of the local rocking curves in some selected regions represented by circular areas of diameter of 96.75 µm (15 pixels), and the map of the full width at half maximum (FWHM) of the local rocking curves in the whole crystal. Generally, digital X-ray topographic images taken with a CCD camera correspond well with X-ray topographic images taken with X-ray films, giving rise to higher contrasts for local defects such as dislocations ( 26 ). The digital X-ray topographic image shows that the crystal is of relatively high quality and dislocation-free.…”

“…A series of digital X-ray topographs were obtained relative to the rotation of the sample crystal. The CCD camera outputs the sequential digital topographic images as 16-bit gray-scale TIFF files.To process the large amount of data in these images, we used the original computer software ( 26 , 35 , 37 ) to obtain mapping of the FWHM and peak position of the local rocking curves over the whole crystal. Further, the local rocking curve profiles were obtained from the reflected intensities in a selected circular area with a diameter of 96.75 μm (15 pixels) of the digital X-ray topographic image.…”

Why Do Protein Crystals Grown With the Aid of Porous Materials Show Better Diffraction Quality?

“…Therefore, we may advance the hypothesis that the misfit between the crystal lattice and the supporting porous material can create grown-in dislocations, leading to a disappearance of local strain in the sub-grainsand thus, improve the diffractivity of the protein crystals. In fact, it has been observed [16] that some dislocations are grown from the seed crystals, chemically cross-linked by glutaraldehyde. Thus, it is logical to assume that the supporting porous material can be far more efficient in creating grown-in dislocations, because the misfit between the crystal lattice and the supporting porous material is greater than in the former case.…”

Radiation-induced defects in protein crystals observed by X-ray topography

“…In pioneering research, the perfection of protein crystals was evaluated using X-ray topography (Fourme et al, 1995;Izumi et al, 1996;Stojanoff & Siddons, 1996;Dobrianov et al, 1998;Boggon et al, 2000;Helliwell, 2005). It has also been successfully applied to characterize grown-in and stress-induced defects in protein crystals (Tachibana et al, 2003;Koishi et al, 2007;Mukobayashi et al, 2009;Suzuki et al, 2021). However, high-quality crystals are required to clarify the pure effects of X-ray irradiation experimentally.…”