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.

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.

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 Organotin(IV) selenate derivatives – Crystal structure of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n

2021 ◽  
Vol 44 (1) ◽  
pp. 213-217
Author(s):  
Waly Diallo ◽  
Hélène Cattey ◽  
Laurent Plasseraud
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Point Of View ◽  
Intermolecular Hydrogen Bonds

Abstract Crystallization of [(Ph3Sn)2SeO4] ⋅ 1.5H2O in methanol leads to the formation of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n (1) which constitutes a new specimen of organotin(IV) selenate derivatives. In the solid state, complex 1 is arranged in polymeric zig-zag chains, composed of alternating Ph3Sn and SeO4 groups. In addition, pendant Ph3Sn ⋅ CH3OH moieties are branched along chains according to a syndiotactic organization and via Sn-O-Se connections. From a supramolecular point of view, intermolecular hydrogen bonds established between the selenate groups (uncoordinated oxygen) and the hydroxyl functions (CH3OH) of the pendant groups link the chains together.

scholarly journals FEBID 3D-Nanoprinting at Low Substrate Temperatures: Pushing the Speed While Keeping the Quality

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1527
Author(s):  
Jakob Hinum-Wagner ◽  
David Kuhness ◽  
Gerald Kothleitner ◽  
Robert Winkler ◽  
Harald Plank
Keyword(s):  
Volume Growth ◽  
Point Of View ◽  
High Fidelity ◽  
Direct Write ◽  
General Picture ◽  
3D Space ◽  
Design Flexibility ◽  
Substrate Temperatures ◽  
Very High ◽  
Comprehensive Discussion

High-fidelity 3D printing of nanoscale objects is an increasing relevant but challenging task. Among the few fabrication techniques, focused electron beam induced deposition (FEBID) has demonstrated its high potential due to its direct-write character, nanoscale capabilities in 3D space and a very high design flexibility. A limitation, however, is the low fabrication speed, which often restricts 3D-FEBID for the fabrication of single objects. In this study, we approach that challenge by reducing the substrate temperatures with a homemade Peltier stage and investigate the effects on Pt based 3D deposits in a temperature range of 5–30 °C. The findings reveal a volume growth rate boost up to a factor of 5.6, while the shape fidelity in 3D space is maintained. From a materials point of view, the internal nanogranular composition is practically unaffected down to 10 °C, followed by a slight grain size increase for even lower temperatures. The study is complemented by a comprehensive discussion about the growth mechanism for a more general picture. The combined findings demonstrate that FEBID on low substrate temperatures is not only much faster, but practically free of drawbacks during high fidelity 3D nanofabrication.

ChemInform Abstract: SnCl4(4-tBuC6H4CHO)2. X-Ray Crystal Structure, Solution NMR, and Implications for Reactions at Complexed Carbonyls.

ChemInform ◽  
1987 ◽  
Vol 18 (34) ◽  
Author(s):  
S. E. DENMARK ◽  
B. R. HENKE ◽  
E. WEBER
Keyword(s):  
Crystal Structure ◽  
Solution Nmr ◽  
X Ray ◽  
Structure Solution

scholarly journals Insulation Characteristics of Sisal Fibre/Epoxy Composites

2017 ◽  
Vol 2017 ◽  
pp. 1-6 ◽  
Author(s):  
A. Shalwan ◽  
M. Alajmi ◽  
A. Alajmi
Keyword(s):  
Volume Fraction ◽  
Fibre Volume Fraction ◽  
Thermal Characteristics ◽  
Fibre Volume ◽  
Point Of View ◽  
Natural Fibres ◽  
Epoxy Composites ◽  
Ongoing Research ◽  
Sisal Fibre ◽  
The Impact

Using natural fibres in civil engineering is the aim of many industrial and academics sectors to overcome the impact of synthetic fibres on environments. One of the potential applications of natural fibres composites is to be implemented in insulation components. Thermal behaviour of polymer composites based on natural fibres is recent ongoing research. In this article, thermal characteristics of sisal fibre reinforced epoxy composites are evaluated for treated and untreated fibres considering different volume fractions of 0–30%. The results revealed that the increase in the fibre volume fraction increased the insulation performance of the composites for both treated and untreated fibres. More than 200% insulation rate was achieved at the volume fraction of 20% of treated sisal fibres. Untreated fibres showed about 400% insulation rate; however, it is not recommended to use untreated fibres from mechanical point of view. The results indicated that there is potential of using the developed composites for insulation purposes.

scholarly journals The Rietveld Refinement in the EXPO Software: A Powerful Tool at the End of the Elaborate Crystal Structure Solution Pathway

Crystals ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 203 ◽  
Author(s):  
Angela Altomare ◽  
Francesco Capitelli ◽  
Nicola Corriero ◽  
Corrado Cuocci ◽  
Aurelia Falcicchio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rietveld Refinement ◽  
Structure Solution

New similarity index for crystal structure determination from X-ray powder diagrams

2005 ◽  
Vol 38 (6) ◽  
pp. 861-866 ◽  
Author(s):  
Detlef Walter Maria Hofmann ◽  
Ludmila Kuleshova
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Similarity Index ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Organic Pigments ◽  
Structure Solution ◽  
Similarity Indices

A new similarity index for automated comparison of powder diagrams is proposed. In contrast to traditionally used similarity indices, the proposed method is valid in cases of large deviations in the cell constants. The refinement according to this index closes the gap between crystal structure prediction and automated crystal structure determination. The opportunities of the new procedure have been demonstrated by crystal structure solution of un-indexed powder diagrams of some organic pigments (PY111, PR181 and Me-PR170).

The Role of Nuclear Stiffness and Resilience in Mechanotransduction

2010 ◽  
Author(s):  
Kris Noel Dahl ◽  
Elizabeth A. Booth-Gauthier ◽  
Alexandre J. S. Ribeiro ◽  
Zhixia Zhong
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Live Cell Imaging ◽  
Volume Fraction ◽  
Direct Role ◽  
Intact Cells ◽  
Large Volume Fraction ◽  
Nuclear Mechanics ◽  
Model Cell

Mechanical force is found to be increasingly important during development and for proper homeostatic maintenance of cells and tissues. The nucleus occupies a large volume fraction of the cell and is interconnected with the cytoskeleton. Here, to determine the direct role of the nucleus itself in converting forces to changes in gene expression, also known as, mechanotransduction, we examine changes in nuclear mechanics and gene reorganization associated with cell fate and with extracellular force. We measure mechanics of nuclei in many model cell systems using micropipette aspiration to show changes in nuclear mechanics. In intact cells we characterize the rheological changes induced in the genome organization with live cell imaging and particle tracking, and we suggest how these changes relate to gene expression.

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