Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Anomalous diffraction in crystallographic phase evaluation.

ABSTRACT: X-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, the methods of MAD (multiwavelength anomalous diffraction) and SAD (single-wavelength anomalous diffraction) now predominate for de novo determinations of atomic-level biological structures. This review describes the physical underpinnings of anomalous diffraction methods, the evolution of these methods to their current maturity, the elements, procedures and instrumentation used for effective implementation, and the realm of applications.

SUBMITTER: Hendrickson WA

PROVIDER: S-EPMC4128195 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Anomalous diffraction in crystallographic phase evaluation.

Hendrickson Wayne A WA

Quarterly reviews of biophysics 20140201 1

X-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, ...[more]

PMID: 24726017

Similar Datasets

Crystallographic anomalous diffraction data for the experimental phasing of two myelin proteins, gliomedin and periaxin.

Project description:We present datasets that can be used for the experimental phasing of crystal structures of two myelin proteins. The structures were recently described in the articles "Periaxin and AHNAK nucleoprotein 2 form intertwined homodimers through domain swapping" (H. Han, P. Kursula, 2014) [1] and "The olfactomedin domain from gliomedin is a β-propeller with unique structural properties" (H. Han, P. Kursula, 2015) [2]. Crystals of periaxin were derivatized with tungsten and xenon prior to data collection, and diffraction data for these crystals are reported at 3 and 1 wavelengths, respectively. Crystallographic data for two different pressurizing times for xenon are provided. Gliomedin was derivatized with platinum, and data for single-wavelength anomalous dispersion are included. The data can be used to repeat the phasing experiments, to analyze heavy atom binding sites in proteins, as well as to optimize future derivatization experiments of protein crystals with these and other heavy-atom compounds.

| S-EPMC5567927 | biostudies-literature

Macromolecular structure phasing by neutron anomalous diffraction.

Project description:In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrated through the use of a state-of-the-art monochromatic neutron diffractometer at the Institut Laue-Langevin (ILL) in combination with crystals of perdeuterated protein that minimise the level of hydrogen incoherent scattering and enhance the visibility of the anomalous signal. The protein used was rubredoxin in which cadmium replaced the iron at the iron-sulphur site. While this study was carried out using a steady-state neutron beam source, the results will be of major interest for capabilities at existing and emerging spallation neutron sources where time-of-flight instruments provide inherent energy discrimination. In particular this capability may be expected to offer unique opportunities to a rapidly developing structural biology community where there is increasing interest in the identification of protonation states, protein/water interactions and protein-ligand interactions - all of which are of central importance to a wide range of fundamental and applied areas in the biosciences.

| S-EPMC4980602 | biostudies-literature

Structures from anomalous diffraction of native biological macromolecules.

Project description:Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.

| S-EPMC3769101 | biostudies-literature

Multi-crystal anomalous diffraction for low-resolution macromolecular phasing.

Project description:Multiwavelength anomalous diffraction (MAD) and single-wavelength anomalous diffraction (SAD) are the two most commonly used methods for de novo determination of macromolecular structures. Both methods rely on the accurate extraction of anomalous signals; however, because of factors such as poor intrinsic order, radiation damage, inadequate anomalous scatterers, poor diffraction quality and other noise-causing factors, the anomalous signal from a single crystal is not always good enough for structure solution. In this study, procedures for extracting more accurate anomalous signals by merging data from multiple crystals are devised and tested. SAD phasing tests were made with a relatively large (1456 ordered residues) poorly diffracting (d(min) = 3.5?Å) selenomethionyl protein (20 Se). It is quantified that the anomalous signal, success in substructure determination and accuracy of phases and electron-density maps all improve with an increase in the number of crystals used in merging. Structure solutions are possible when no single crystal can support structural analysis. It is proposed that such multi-crystal strategies may be broadly useful when only weak anomalous signals are available.

| S-EPMC3016016 | biostudies-literature

Bayesian machine learning improves single-wavelength anomalous diffraction phasing.

Project description:Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.

| S-EPMC6833979 | biostudies-literature

Revealing redox isomerism in trichromium imides by anomalous diffraction.

Project description:In polynuclear biological active sites, multiple electrons are needed for turnover, and the distribution of these electrons among the metal sites is affected by the structure of the active site. However, the study of the interplay between structure and redox distribution is difficult not only in biological systems but also in synthetic polynuclear clusters since most redox changes produce only one thermodynamically stable product. Here, the unusual chemistry of a sterically hindered trichromium complex allowed us to probe the relationship between structural and redox isomerism. Two structurally isomeric trichromium imides were isolated: asymmetric terminal imide (tbsL)Cr3(NDipp) and symmetric, μ3-bridging imide (tbsL)Cr3(μ3-NBn) ((tbsL)6- = (1,3,5-C6H9(NC6H4-o-NSi t BuMe2)3)6-). Along with the homovalent isocyanide adduct (tbsL)Cr3(CNBn) and the bisimide (tbsL)Cr3(μ3-NPh)(NPh), both imide isomers were examined by multiple-wavelength anomalous diffraction (MAD) to determine the redox load distribution by the free refinement of atomic scattering factors. Despite their compositional similarities, the bridging imide shows uniform oxidation of all three Cr sites while the terminal imide shows oxidation at only two Cr sites. Further oxidation from the bridging imide to the bisimide is only borne at the Cr site bound to the second, terminal imido fragment. Thus, depending on the structural motifs present in each [Cr3] complex, MAD revealed complete localization of oxidation, partial localization, and complete delocalization, all supported by the same hexadentate ligand scaffold.

| S-EPMC8654065 | biostudies-literature

Crystallographic characterization of steel microstructure using neutron diffraction.

Project description:Applications of neutron diffraction to microstructure evaluation of steel investigated by a project commissioned by the Innovative Structural Materials Association are summarized. The volume fraction of austenite (γ) for a 1.5Mn-1.5Si-0.2C steel was measured by various techniques including backscatter electron diffraction (EBSD) and X-ray diffraction. It is recommended to measure volume fraction and texture simultaneously using neutron diffraction. The γ reverse transformation was in situ monitored using dilatometry, EBSD, X-ray diffraction and neutron diffraction. The γ reversion kinetics showed excellent agreements between dilatometry and neutron diffraction, whereas the γ formation started at higher temperatures in EBSD and X-ray diffraction measurements. Such discrepancy is attributed to the change in chemical compositions at the specimen surface by heating; Mn and C concentrations were decreased with heating. Phase transformations from γ upon cooling were monitored, which enabled us to elucidate the changes in lattice parameters of ferrite (α) and γ affected by not only thermal contraction but also transformation strains, thermal misfit strains and carbon enrichment in γ in the above hypoeutectoid steel. Pearlitic transformation started after the carbon enrichment reached approximately 0.76 mass% and contributed to diffraction line broadening. Martensitic transformation with or without ausforming at 700°C was monitored for a medium carbon low alloyed steel. Dislocation density after ausforming was determined using the convolutional multiple whole profile fitting method for 10 s time-sliced data. The changes in γ and martensite lattice parameters upon quenching were tracked and new insights on internal stresses and the axial ratio of martensite were obtained.

| S-EPMC7008240 | biostudies-literature

Anomalous X-ray diffraction studies of ion transport in K+ channels.

Project description:Potassium ion channels utilize a highly selective filter to rapidly transport K+ ions across cellular membranes. This selectivity filter is composed of four binding sites which display almost equal electron density in crystal structures with high potassium ion concentrations. This electron density can be interpreted to reflect a superposition of alternating potassium ion and water occupied states or as adjacent potassium ions. Here, we use single wavelength anomalous dispersion (SAD) X-ray diffraction data collected near the potassium absorption edge to show experimentally that all ion binding sites within the selectivity filter are fully occupied by K+ ions. These data support the hypothesis that potassium ion transport occurs by direct Coulomb knock-on, and provide an example of solving the phase problem by K-SAD.

| S-EPMC6208422 | biostudies-literature

Multiwavelength anomalous diffraction analysis at the M absorption edges of uranium.

Project description:The multiwavelength anomalous diffraction (MAD) method for phase evaluation is now widely used in macromolecular crystallography. Successful MAD structure determinations have been carried out at the K or L absorption edges of a variety of elements. In this study, we investigate the anomalous scattering properties of uranium at its M(IV) (3.326 A) and M(V) (3.490 A) edge. Fluorescence spectra showed remarkably strong anomalous scattering at these edges (f' = -70e, f" = 80e at the M(IV) edge and f' = -90e, f" = 105e at the M(V) edge), many times higher than from any anomalous scatterers used previously for MAD phasing. However, the large scattering angles and high absorption at the low energies of these edges present some difficulties not found in typical crystallographic studies. We conducted test experiments at the M(IV) edge with crystals of porcine elastase derivatized with uranyl nitrate. A four-wavelength MAD data set complete to 3.2-A Bragg spacings was collected from a single small frozen crystal. Analysis of the data yielded satisfactory phase information (average difference of (0)phi(T) - (0)phi(A) for replicated determinations is 32 degrees ) and produced an interpretable electron-density map. Our results demonstrate that it is practical to measure macromolecular diffraction data at these edges with current instrumentation and that phase information of good accuracy can be extracted from such experiments. We show that such experiments have potential for the phasing of very large macromolecular assemblages.

| S-EPMC58520 | biostudies-literature

Three-beam convergent-beam electron diffraction for measuring crystallographic phases.

Project description:Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes. The octant, in which the three-phase invariant lies, can be determined simply by inspection of the indexed CBED patterns (i.e. the uncertainty of the phase measurement is ±22.5°). This approach is demonstrated with the experimental measurement of three-phase invariants in two simple test cases: centrosymmetric Si and non-centrosymmetric GaAs. This method may complement existing structure determination methods by providing direct measurements of three-phase invariants to replace 'guessed' invariants in ab initio phasing methods and hence provide more stringent constraints to the structure solution.

| S-EPMC6211523 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data