scholarly journals Dealing with Aperiodic Protein Crystal Structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C778-C778
Author(s):  
Gloria Borgstahl
Keyword(s):  
Three Dimensional ◽  
Protein Crystal ◽  
Periodic Lattice ◽  
X Rays ◽  
Future Directions ◽  
Space Group ◽  
3D Space ◽  
Structure Solution ◽  
Quasi Crystals ◽  
Aperiodic Crystals

Protein crystals can be aperiodic. They will diffract X-rays, and are therefore a crystal, but their diffraction is not periodic. This means that their diffraction pattern cannot be simply be indexed by a typical three-dimensional unit cell and space group. Aperiodic crystals include "quasi-crystals" as well as "modulated" crystals. In the latter case, the modulation can be positional or occupational and these modulations can be incommensurate with the normal periodic lattice [1]. An overview of aperiodic protein crystal diffraction will be presented with examples. The discussion will then focus on the characteristics of incommensurately modulated crystals followed by a more detailed discussion of how to solve these crystals. The following details of structure solution will be presented: (1) data collection perils; (2) specialized diffraction data processing in (3+1)D space using a q-vector [2]; (3) how to get an approximation of the structure in 3D space; (4) the assignment of the (3+1)D space group; and the ultimate (5) crystallographic refinement in superspace[3]. Future directions and needs will be discussed.

scholarly journals How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal

2017 ◽  
Vol 50 (4) ◽  
pp. 1200-1207 ◽  
Author(s):  
Jason Porta ◽  
Jeff Lovelace ◽  
Gloria E. O. Borgstahl
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Real Life ◽  
Group Symmetry ◽  
Protein Crystal ◽  
3D Space ◽  
Structure Solution ◽  
Crystallographic Symmetry ◽  
Aperiodic Crystals ◽  
Periodic Crystal

Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and requireqvectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C ofInternational Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal.

Modified Nextal crystallization device forin situinspection of protein crystal quality

2005 ◽  
Vol 38 (2) ◽  
pp. 396-397 ◽  
Author(s):  
Nobuhisa Watanabe
Keyword(s):  
Crystal Quality ◽  
Protein Crystal ◽  
X Rays ◽  
Resolution Limit ◽  
Physical Damage ◽  
Space Group ◽  
Cell Parameters

The modification and use of the Nextal crystallization device for checking the diffraction quality of protein crystalsin situis described. Using the modified device, crystals in the crystallization drop can be exposed to X-rays directly to observe the diffraction quality without physical damage to the crystal. If the crystals in the drop are well separated, not only the resolution limit of the crystal is estimated, but also determination of the space group and the cell parameters is possible.

EDMA: a computer program for topological analysis of discrete electron densities

2012 ◽  
Vol 45 (3) ◽  
pp. 575-580 ◽  
Author(s):  
Lukáš Palatinus ◽  
Siriyara Jagannatha Prathapa ◽  
Sander van Smaalen
Keyword(s):  
Computer Program ◽  
Electron Density ◽  
Critical Points ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Real Space ◽  
Principal Curvatures ◽  
Electron Densities ◽  
Structure Solution ◽  
Aperiodic Crystals

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

Crystallography of quasi-crystals

1986 ◽  
Vol 42 (4) ◽  
pp. 261-271 ◽  
Author(s):  
T. Janssen
Keyword(s):  
Three Dimensional ◽  
Three Dimensions ◽  
Crystal Phase ◽  
Two Dimensional ◽  
Space Group ◽  
Quasi Crystals ◽  
Special Case

The symmetry of quasi-crystals, a class of materials that has recently aroused interest, is discussed. It is shown that a quasi-crystal is a special case of an incommensurate crystal phase and that it can be described by a space group in more than three dimensions. A number of relevant three-dimensional quasi-crystals is discussed, in particular dihedral and icosahedral structures. The symmetry considerations are also applied to the two-dimensional Penrose patterns.

scholarly journals Reducing dynamical electron scattering reveals hydrogen atoms

2019 ◽  
Vol 75 (1) ◽  
pp. 82-93 ◽  
Author(s):  
Max T. B. Clabbers ◽  
Tim Gruene ◽  
Eric van Genderen ◽  
Jan Pieter Abrahams
Keyword(s):  
Electron Scattering ◽  
Crystal Size ◽  
Protein Crystal ◽  
X Rays ◽  
Pixel Detector ◽  
Hydrogen Atoms ◽  
Structure Solution ◽  
Highly Sensitive ◽  
Improved Model ◽  
Dynamic Scattering

Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.

scholarly journals A crystallographic study of human NONO (p54nrb): overcoming pathological problems with purification, data collection and noncrystallographic symmetry

2016 ◽  
Vol 72 (6) ◽  
pp. 761-769 ◽  
Author(s):  
Gavin J. Knott ◽  
Santosh Panjikar ◽  
Andrea Thorn ◽  
Archa H. Fox ◽  
Maria R. Conte ◽  
...  
Keyword(s):  
Data Collection ◽  
Nuclear Gene ◽  
Beam Width ◽  
Molecular Replacement ◽  
X Rays ◽  
Space Group ◽  
Pou Domain ◽  
Structure Solution ◽  
Oriented Parallel ◽  
Nuclear Gene Regulation

Non-POU domain-containing octamer-binding protein (NONO, a.k.a. p54nrb) is a central player in nuclear gene regulation with rapidly emerging medical significance. NONO is a member of the highly conservedDrosophilabehaviour/human splicing (DBHS) protein family, a dynamic family of obligatory dimeric nuclear regulatory mediators. However, work with the NONO homodimer has been limited by rapid irreversible sample aggregation. Here, it is reported that L-proline stabilizes purified NONO homodimers, enabling good-quality solution small-angle X-ray structure determination and crystallization. NONO crystallized in the apparent space groupP21with a unique axis (b) of 408.9 Å and with evidence of twinning, as indicated by the cumulative intensity distributionLstatistic, suggesting the possibility of space groupP1. Structure solution by molecular replacement shows a superhelical arrangement of six NONO homodimers (or 12 inP1) oriented parallel to the long axis, resulting in extensive noncrystallographic symmetry. Further analysis revealed that the crystal was not twinned, but the collected data suffered from highly overlapping reflections that obscured theL-test. Optimized data collection on a new crystal using higher energy X-rays, a smaller beam width and an increased sample-to-detector distance produced non-overlapping reflections to 2.6 Å resolution. The steps taken to analyse and overcome this series of practical difficulties and to produce a biologically informative structure are discussed.

scholarly journals Crystal pathologies in macromolecular crystallography

2016 ◽  
Vol 62 (3) ◽  
pp. 401-407
Author(s):  
Zbigniew Dauter ◽  
Mariusz Jaskólski
Keyword(s):  
Crystal Structure ◽  
Volume Fraction ◽  
Poor Quality ◽  
Point Of View ◽  
Periodic Lattice ◽  
Lattice Order ◽  
Large Volume Fraction ◽  
3D Space ◽  
Structure Solution ◽  
Physical Defects

Macromolecules, such as proteins or nucleic acids, form crystals with a large volume fraction of water, ~50% on average. Apart from typical physical defects and rather trivial poor quality problems, macromolecular crystals, as essentially any crystals, can also suffer from several kinds of pathologies, in which everything seems to be perfect, except that from the structural point of view the interpretation may be very difficult, sometimes even im-possible. A frequent nuisance is pseudosymmetry, or non-crystallographic symmetry (NCS), which is particularly nasty when it has translational character. Lattice-translocation defects, also called order-disorder twinning (OD-twinning), occur when molecules are packed regularly in layers but the layers are stacked (without rotation) in two (or more) discrete modes, with a unique translocation vector. Crystal twinning arises when twin domains have different orientations, incompatible with the symmetry of the crystal structure. There are also crystals in which the periodic (lattice) order is broken or absent altogether. When the strict short-range translational order from one unit cell to the next is lost but the long-range order is restored by a periodic modulation, we have a modulated crystal structure. In quasicrystals (not observed for macromolecules yet), the periodic order (in 3D space) is lost completely and the diffraction pattern (which is still discrete) cannot be even indexed using three hkl indices. In addition, there are other physical defects and phenomena (such as high mosaicity, diffraction anisotropy, diffuse scattering, etc.) which make diffraction data processing and structure solution difficult or even impossible.

Measurements in 3D images

1991 ◽  
Vol 49 ◽  
pp. 408-409
Author(s):  
John C. Russ
Keyword(s):  
Three Dimensional ◽  
Image Plane ◽  
X Rays ◽  
Traditional Use ◽  
3D Images ◽  
Confocal Scanning Laser Microscope ◽  
Hard Materials ◽  
Depth Direction ◽  
Confocal Scanning ◽  
Confocal Scanning Laser

Three-dimensional (3D) images consisting of arrays of voxels can now be routinely obtained from several different types of microscopes. These include both the transmission and emission modes of the confocal scanning laser microscope (but not its most common reflection mode), the secondary ion mass spectrometer, and computed tomography using electrons, X-rays or other signals. Compared to the traditional use of serial sectioning (which includes sequential polishing of hard materials), these newer techniques eliminate difficulties of alignment of slices, and maintain uniform resolution in the depth direction. However, the resolution in the z-direction may be different from that within each image plane, which makes the voxels non-cubic and creates some difficulties for subsequent analysis.

Other topics

2018 ◽  
Author(s):  
Ted Janssen ◽  
Gervais Chapuis ◽  
Marc de Boissieu
Keyword(s):  
Photonic Crystals ◽  
Crystal Morphology ◽  
Three Dimensional ◽  
Icosahedral Quasicrystal ◽  
Crystal Surfaces ◽  
Decagonal Quasicrystal ◽  
System A ◽  
Fundamental Law ◽  
Quasiperiodic Systems ◽  
Aperiodic Crystals

The law of rational indices to describe crystal faces was one of the most fundamental law of crystallography and is strongly linked to the three-dimensional periodicity of solids. This chapter describes how this fundamental law has to be revised and generalized in order to include the structures of aperiodic crystals. The generalization consists in using for each face a number of integers, with the number corresponding to the rank of the structure, that is, the number of integer indices necessary to characterize each of the diffracted intensities generated by the aperiodic system. A series of examples including incommensurate multiferroics, icosahedral crystals, and decagonal quaiscrystals illustrates this topic. Aperiodicity is also encountered in surfaces where the same generalization can be applied. The chapter discusses aperiodic crystal morphology, including icosahedral quasicrystal morphology, decagonal quasicrystal morphology, and aperiodic crystal surfaces; magnetic quasiperiodic systems; aperiodic photonic crystals; mesoscopic quasicrystals, and the mineral calaverite.

scholarly journals Design, Fabrication, and Testing of a Novel 3D 3-Fingered Electrothermal Microgripper with Multiple Degrees of Freedom

Micromachines ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 444
Author(s):  
Guoning Si ◽  
Liangying Sun ◽  
Zhuo Zhang ◽  
Xuping Zhang
Keyword(s):  
Degrees Of Freedom ◽  
Dynamic Properties ◽  
Three Dimensional ◽  
Polyimide Film ◽  
Zebrafish Embryos ◽  
Multiple Degrees Of Freedom ◽  
Electrothermal Actuator ◽  
3D Space ◽  
Pick And Place

This paper presents the design, fabrication, and testing of a novel three-dimensional (3D) three-fingered electrothermal microgripper with multiple degrees of freedom (multi DOFs). Each finger of the microgripper is composed of a V-shaped electrothermal actuator providing one DOF, and a 3D U-shaped electrothermal actuator offering two DOFs in the plane perpendicular to the movement of the V-shaped actuator. As a result, each finger possesses 3D mobilities with three DOFs. Each beam of the actuators is heated externally with the polyimide film. The durability of the polyimide film is tested under different voltages. The static and dynamic properties of the finger are also tested. Experiments show that not only can the microgripper pick and place microobjects, such as micro balls and even highly deformable zebrafish embryos, but can also rotate them in 3D space.

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