Search results for "structure determination"
showing 10 items of 19 documents
Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study
2018
Single-molecule Forster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between +/- 0.02 and +/- 0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and…
Preparation and molecular structures of N′-(2-heteroarylmethylidene)-3-(3-pyridyl)acrylohydrazides
2018
Abstract The crystal and molecular structures of N′-(2-furylmethylidene)-3-(3-pyridyl)acrylohydrazide and N′-(2-thienylmethylidene)-3-(3-pyridyl)acrylohydrazide are reported, and the influence of the type of the heteroatom on the aromaticity of the aromatic rings is discussed. Both molecules are nearly planar. The geometry of the acrylohydrazide arrangement is comparable to that of homologous compounds. Density functional theory (DFT) calculations were performed in order to analyze the changes in the geometry of the studied compounds in the crystalline state and for the isolated molecule. The most significant changes were observed in the values of the N–N and C–N bond lengths. The harmonic …
Analysis of the structural quality of the CASD-NMR 2013 entries
2015
We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from t…
Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition
2018
The co-crystal structure of the metallopeptidase astacin with its specific protein inhibitor fetuin-B reveals a novel mechanism of inhibition.
Mono- and Binuclear Copper(II) and Nickel(II) Complexes with the 3,6-Bis(picolylamino)-1,2,4,5-Tetrazine Ligand
2021
Four new compounds of formulas [Cu(hfac)2(L)] (1), [Ni(hfac)2(L)] (2), [{Cu(hfac)2}2(µ-L)]·2CH3OH (3) and [{Ni(hfac)2}2(µ-L)]·2CH3CN (4) [Hhfac = hexafluoroacetylacetone and L = 3,6-bis(picolylamino)-1,2,4,5-tetrazine] have been prepared and their structures determined by X-ray diffraction on single crystals. Compounds 1 and 2 are isostructural mononuclear complexes where the metal ions [copper(II) (1) and nickel(II) (2)] are six-coordinated in distorted octahedral MN2O4 surroundings which are built by two bidentate hfac ligands plus another bidentate L molecule. This last ligand coordinates to the metal ions through the nitrogen atoms of the picolylamine fragment. Compounds 3 and 4 are cen…
3D Electron Diffraction: The Nanocrystallography Revolution
2019
Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook review…
Automated electron diffraction tomography - a new tool for nano crystal structure analysis
2011
Automated electron Diffraction Tomography (ADT) comprises an upcoming method for “ab intio” structure analysis of nano crystals. ADT allows fine sampling of the reciprocal space by sequential collection of electron diffraction patterns while tilting a nano crystal in fixed tilt steps around an arbitrary axis. Electron diffraction is collected in nano diffraction mode (NED) with a semi-parallel beam with a diameter down to 50 nm. For crystal tracking micro-probe STEM imaging is used. Full automation of the acquisition procedure allowed optimisation of the electron dose distribution and therefore analysis of highly beam sensitive samples. Cell parameters, space group and reflection intensitie…
Ab Initio Structure Determination of Vaterite by Automated Electron Diffraction
2012
tion that is fundamental for understanding material properties. Still, a number of compounds have eluded such kinds of analysis because they are nanocrystalline, highly disordered, with strong pseudosymmetries or available only in small amounts in polyphasic or polymorphic systems. These materials are crystallographically intractable with conventional Xray or synchrotron radiation diffraction techniques. Single nanoparticles can be visualized by high-resolution transmission electron microscopy (HR-TEM) up to sub�ngstrom resolution, [2] but obtaining 3D information is still a difficult task, especially for highly beam-sensitive materials and crystal structures with long cell parameters. Elec…
Structure solution of zeolites by automated electron diffraction tomography - Impact and treatment of preferential orientation
2014
Abstract In this paper the reliability of structure solution of nano-crystalline porous compounds with preferred orientation based on automated electron diffraction tomography (ADT) is discussed. It will be shown that the limitations of the data acquisition geometry can be overcome by completing the missing diffraction data with additional diffraction information. Apart from different ways of sample preparation, data merging with either additional ADT data sets or intensities derived from X-ray powder diffraction comprise an effective way to improve the accuracy of the structure solution.
Applications of automated diffraction tomography (ADT) on nanocrystalline porous materials
2013
Abstract Many porous materials, both inorganic and hybrid organic–inorganic, can only be synthesized as nanocrystals. X-ray powder diffraction delivers one-dimensional data from the overall sample and is therefore often limited by peak overlap at low or medium resolution and by peak broadening. Thus, structure solution of materials with large unit cells and low symmetry, disorder or pseudosymmetry, or available only in polyphasic systems, turns out to be problematic or even impossible. Electron diffraction allows collecting three-dimensional structure information from nanocrystalline materials, but is traditionally biased by low completeness of the diffraction data, dynamical scattering and…