scholarly journals Maximum-likelihood determination of anomalous substructures

2018 ◽  
Vol 74 (2) ◽  
pp. 98-105 ◽  
Author(s):  
Randy J. Read ◽  
Airlie J. McCoy
Keyword(s):  
Fourier Transform ◽  
Maximum Likelihood ◽  
Measurement Errors ◽  
Dual Space ◽  
Anomalous Scattering ◽  
X Ray ◽  
Sad Phasing ◽  
Improve Determination ◽  
Proof Of Principle

A fast Fourier transform (FFT) method is described for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by X-ray single-wavelength anomalous diffraction (SAD). This method is based on the maximum-likelihood SAD phasing function, which accounts for measurement errors and for correlations between the observed and calculated Bijvoet mates. Proof of principle is shown that this method can improve determination of the anomalously scattering substructure in challenging cases where the anomalous scattering from the substructure is weak but the substructure also constitutes a significant fraction of the real scattering. The method is deterministic and can be fast compared with existing multi-trial dual-space methods for SAD substructure determination.

scholarly journals Long-wavelength native-SAD phasing: opportunities and challenges

IUCrJ ◽  
2019 ◽  
Vol 6 (3) ◽  
pp. 373-386 ◽  
Author(s):  
Shibom Basu ◽  
Vincent Olieric ◽  
Filip Leonarski ◽  
Naohiro Matsugaki ◽  
Yoshiaki Kawano ◽  
...  
Keyword(s):  
Anomalous Scattering ◽  
X Rays ◽  
X Ray ◽  
Long Wavelength ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Scattering Factor ◽  
X Ray Absorption

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

scholarly journals Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data

IUCrJ ◽  
2016 ◽  
Vol 3 (3) ◽  
pp. 180-191 ◽  
Author(s):  
Karol Nass ◽  
Anton Meinhart ◽  
Thomas R. M. Barends ◽  
Lutz Foucar ◽  
Alexander Gorel ◽  
...  
Keyword(s):  
Structure Determination ◽  
Free Electron ◽  
De Novo ◽  
Protein Structure Determination ◽  
Anomalous Scattering ◽  
X Ray ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL datade novois complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.

Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography

2011 ◽  
Vol 19 (1) ◽  
pp. 19-29 ◽  
Author(s):  
James Doutch ◽  
Michael A. Hough ◽  
S. Samar Hasnain ◽  
Richard W. Strange
Keyword(s):  
Model Building ◽  
De Novo ◽  
Protein Structures ◽  
Anomalous Scattering ◽  
X Ray ◽  
Long Wavelength ◽  
Structure Solution ◽  
Average Proportion ◽  
Sad Phasing

The sulfur SAD phasing method allows the determination of protein structuresde novowithout reference to derivatives such as Se-methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimericAchromobacter cycloclastesnitrite reductase (AcNiR), which contains a near average proportion of sulfur-containing residues and two Cu atoms per subunit. Experiments using X-ray wavelengths in the range 1.9–2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful forautomatedstructure solution and model building using existing beamlines and current software tools. On the other hand, experiments using the shortest X-ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long-wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ∼1.25% at ∼2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ∼0.75 Å) forAcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.

scholarly journals Determination of crystallographic intensities from sparse data

IUCrJ ◽  
2015 ◽  
Vol 2 (1) ◽  
pp. 29-34 ◽  
Author(s):  
Kartik Ayyer ◽  
Hugh T. Philipp ◽  
Mark W. Tate ◽  
Jennifer L. Wierman ◽  
Veit Elser ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Crystal Size ◽  
Three Dimensional ◽  
Sparse Data ◽  
Data Sets ◽  
X Rays ◽  
Diffraction Intensity ◽  
X Ray ◽  
Proof Of Principle

X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. TheEMCalgorithm [Loh & Elser (2009),Phys. Rev. E,80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philippet al.(2012),Opt. Express,20, 13129–13137; Ayyeret al.(2014),Opt. Express,22, 2403–2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35 kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.

Determination of the Cation Distribution in NiFe2(PO4)2 using Resonant X-ray and Neutron Powder Diffraction

1995 ◽  
Vol 28 (5) ◽  
pp. 494-502 ◽  
Author(s):  
J. K. Warner ◽  
A. K. Cheetham ◽  
D. E. Cox
Keyword(s):  
Powder Diffraction ◽  
National Laboratory ◽  
Time Of Flight ◽  
Brookhaven National Laboratory ◽  
Neutron Powder Diffraction ◽  
Anomalous Scattering ◽  
Edge Structure ◽  
X Ray ◽  
Scattering Correction

The distribution of divalent iron and nickel over two metal sites of differing coordination geometry in NiFe2(PO4)2, sarcopside, has been investigated by resonant X-ray and time-of-flight neutron powder diffraction. To assess the reproducibility of the X-ray technique, data have been collected from instruments X7A at Brookhaven National Laboratory and 8.3 at the Synchrotron Radiation Source, Daresbury Laboratory, England, using wavelengths λ X1 = 1.7437 (3) Å and λ X2 = 1.7434 (1) Å, respectively, close to the Fe2+ K edge determined by X-ray absorption near-edge structure. The real part of the anomalous-scattering correction for iron at each energy, f′(Fe) X1 = −7.81 (9) and f′(Fe) X2 = −10.16 (6), was determined experimentally by diffraction from Fe3(PO4)2 under identical conditions. Occupancies obtained for iron at the M(1) site were found to be M(1) X1 = 0.366 (6) and M(1) X2 = 0.376 (3), compared with M(1) N = 0.26 (15) from time-of-flight neutron powder diffraction.

Differential Anomalous X-Ray Scattering Techniques for Determination of Liquid and Amorphous Structures

1985 ◽  
Vol 57 ◽  
Author(s):  
W. K. Warburton ◽  
K. F. Ludwig ◽  
L. Wilson ◽  
A. Bienenstock
Keyword(s):  
Structural Models ◽  
Distribution Functions ◽  
Anomalous Scattering ◽  
Differential Distribution ◽  
X Ray ◽  
Amorphous Systems ◽  
X Ray Scattering ◽  
Scattering Technique ◽  
Amorphous Structures

AbstractThe differential anomalous scattering technique is outlined and compared to other techniques for studying short-range order in amorphous systems, such as EXAFS. The differential distribution functions obtained for liquid GeBr4 were found to support a model for the liquid state based on the structure of the h.c.p. crystal. Application of the technique to aqueous ZnBr2 also allowed discr imination between structural models.

scholarly journals Contemporary X-ray electron-density studies using synchrotron radiation

IUCrJ ◽  
2014 ◽  
Vol 1 (5) ◽  
pp. 267-280 ◽  
Author(s):  
Mads R. V. Jørgensen ◽  
Venkatesha R. Hathwar ◽  
Niels Bindzus ◽  
Nanna Wahlberg ◽  
Yu-Sheng Chen ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Diffraction Data ◽  
Bragg Diffraction ◽  
Anomalous Scattering ◽  
Future Directions ◽  
X Ray ◽  
Conventional Radiation ◽  
Radiation Sources ◽  
Systematic Effects

Synchrotron radiation has many compelling advantages over conventional radiation sources in the measurement of accurate Bragg diffraction data. The variable photon energy and much higher flux may help to minimize critical systematic effects such as absorption, extinction and anomalous scattering. Based on a survey of selected published results from the last decade, the benefits of using synchrotron radiation in the determination of X-ray electron densities are discussed, and possible future directions of this field are examined.

Determination of anomalous scattering factors in GaAs using x-ray refraction through a prism

1985 ◽  
Vol 31 (6) ◽  
pp. 3599-3605 ◽  
Author(s):  
A. Fontaine ◽  
W. K. Warburton ◽  
K. F. Ludwig
Keyword(s):  
Anomalous Scattering ◽  
X Ray

scholarly journals Determination of sulfur in diesel using ATR/ FTIR and multivariate calibration

2018 ◽  
Vol 35 (2) ◽  
pp. 71
Author(s):  
Itânia Pinheiro Soares ◽  
Thais F. Rezende ◽  
Isabel Cristina Pereira Fortes
Keyword(s):  
Fourier Transform ◽  
Variable Selection ◽  
Sulfur Content ◽  
Multivariate Calibration ◽  
Infrared Spectrometry ◽  
Fourier Transform Infrared Spectrometry ◽  
Standard Methods ◽  
X Ray ◽  
Calibration Models

The aim of this present work was to provide a more fast, simple and less expensive to analyze sulfur content in diesel samples than by the standard methods currently used. Thus, samples of diesel fuel with sulfur concentrations varying from 400 and 2500 mgkg-1 were analyzed by two methodologies: X-ray fluorescence, according to ASTM D4294 and by Fourier transform infrared spectrometry (FTIR). The spectral data obtained from FTIR were used to build multivariate calibration models by partial least squares (PLS). Four models were built in three different ways: 1) a model using the full spectra (665 to 4000 cm-1), 2) two models using some specific spectrum regions and 3) a model with variable selected by classic method of variable selection stepwise. The model obtained by variable selection stepwise and the model built with region spectra between 665 and 856 cm-1 and 1145 and 2717 cm-1 showed better results in the determination of sulfur content.

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