Dataset Information

A new method to reliably determine elastic strain of various crystal structures from atomic-resolution images.

ABSTRACT: Elastic strain engineering is an important strategy to design material properties in semiconductor and emerging advanced manufacturing industries. Recently, peak-pair method has drawn great attention compared to geometric phase analysis, owing to its precise determination of atom position at real space. Most current strain characterization methods estimate the local strain by comparing it with the related information from unstrained areas as reference. However, peak-pair method generated large errors in some cases because of the complexity of lower symmetric crystal structures, such as hexagonal structure. In this study, we introduce a new algorithm to overcome this limitation by directly comparing the atom positions with multiple references with different lattice symmetries. Furthermore, this new method is validated through several complicated crystal systems such as hexagonal, orthorhombic, monoclinic, and tetragonal structure, and returns expected values. This finding is essential to reliably determine the localized elastic strain with various crystal structures.

SUBMITTER: Chen JS

PROVIDER: S-EPMC6856106 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A new method to reliably determine elastic strain of various crystal structures from atomic-resolution images.

Chen J S JS Liu Y Y Zhai Y Y Fan T X TX

Scientific reports 20191114 1

Elastic strain engineering is an important strategy to design material properties in semiconductor and emerging advanced manufacturing industries. Recently, peak-pair method has drawn great attention compared to geometric phase analysis, owing to its precise determination of atom position at real space. Most current strain characterization methods estimate the local strain by comparing it with the related information from unstrained areas as reference. However, peak-pair method generated large e ...[more]

PMID: 31727929

Similar Datasets

Project description:Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(?) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5?Å and more than one third were conserved within 0.1?Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.

Project description:We have used x-ray crystallography to determine the structures of sperm whale myoglobin (Mb) in four different ligation states (unligated, ferric aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better than 1.2 A. Data collection and analysis were performed in as much the same way as possible to reduce model bias in differences between structures. The structural differences among the ligation states are much smaller than previously estimated, with differences of <0.25 A root-mean-square deviation among all atoms. One structural parameter previously thought to vary among the ligation states, the proximal histidine (His-93) azimuthal angle, is nearly identical in all the ferrous complexes, although the tilt of the proximal histidine is different in the unligated form. There are significant differences, however, in the heme geometry, in the position of the heme in the pocket, and in the distal histidine (His-64) conformations. In the CO complex the majority conformation of ligand is at an angle of 18 +/- 3 degrees with respect to the heme plane, with a geometry similar to that seen in encumbered model compounds; this angle is significantly smaller than reported previously by crystallographic studies on monoclinic Mb crystals, but still significantly larger than observed by photoselection. The distal histidine in unligated Mb and in the dioxygenated complex is best described as having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in low-pH structures where His-64 is doubly protonated. We suggest that these conformations of the distal histidine correspond to the different conformational substates of MbCO and MbO(2) seen in vibrational spectra. Full-matrix refinement provides uncertainty estimates of important structural parameters. Anisotropic refinement yields information about correlated disorder of atoms; we find that the proximal (F) helix and heme move approximately as rigid bodies, but that the distal (E) helix does not.

Dataset Information

A new method to reliably determine elastic strain of various crystal structures from atomic-resolution images.

Publications

A new method to reliably determine elastic strain of various crystal structures from atomic-resolution images.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure