X-ray Wavelength (x-ray + wavelength)

Distribution by Scientific Domains

Selected Abstracts

FBR: a robust method to determine the basis matrix of the Bravais lattice from oscillation images

Klaus D÷hring
The FBR (Fourier basis reconstruction) method described in this paper has been designed to determine the basis matrix of the Bravais lattice with respect to the laboratory frame of reference and without prior knowledge of cell constants, particularly for protein crystals of comparatively low quality. It is based on Fourier analysis of a three-dimensional intensity distribution in reciprocal space, which is directly obtained from observed intensity distributions, provided that they are recorded by the rotation method using a fixed X-ray wavelength, resulting in a direct-space determination of the basis vectors. After a description of the motivation and theory behind the method, it is tested by application to numerically generated images of a virtual sample crystal and to experimental data of a lysozyme crystal with well known cell constants. Finally, FBR is applied to a set of images of bacteriorhodopsin crystals suffering from strong anisotropic spot broadening; this case provided the original motivation for the present work. [source]

Two-wavelength inversion of multiply scattered soft X-ray intensities to charge density

J. C. H. Spence
A method is described for reconstructing the two-dimensional real-space charge density of an isolated object from measurement of the soft X-ray transmission diffraction pattern when it is affected by strong multiple scattering. The Bloch-wave scattering-matrix approach is used to show that the diffracted amplitude depends only on a simple product of X-ray wavelength and sample thickness (unlike the case of relativistic electron diffraction) under reasonable approximations. The multislice formulation then gives the effect of a small change in wavelength, which involves only single scattering. Dynamical diffraction patterns are recorded at two adjacent wavelengths, phased by iterative methods, transformed to real space and divided to give a single-scattering wavefunction. This can then be used to produce a charge-density map. The extension of the method to tomography is discussed. Consideration is first also given to the possibility that absorption due to the photoelectric effect may be so severe for soft X-rays that multiple elastic scattering becomes so much less probable than photoelectric absorption that it may be neglected entirely. A discussion of signs in soft X-ray, positron and electron multiple-scattering theory is given. [source]

The minimum crystal size needed for a complete diffraction data set

James M. Holton
In this work, classic intensity formulae were united with an empirical spot-fading model in order to calculate the diameter of a spherical crystal that will scatter the required number of photons per spot at a desired resolution over the radiation-damage-limited lifetime. The influences of molecular weight, solvent content, Wilson B factor, X-ray wavelength and attenuation on scattering power and dose were all included. Taking the net photon count in a spot as the only source of noise, a complete data set with a signal-to-noise ratio of 2 at 2,┼ resolution was predicted to be attainable from a perfect lysozyme crystal sphere 1.2,Ám in diameter and two different models of photoelectron escape reduced this to 0.5 or 0.34,Ám. These represent 15-fold to 700-fold less scattering power than the smallest experimentally determined crystal size to date, but the gap was shown to be consistent with the background scattering level of the relevant experiment. These results suggest that reduction of background photons and diffraction spot size on the detector are the principal paths to improving crystallographic data quality beyond current limits. [source]

Use of Cr K, radiation to enhance the signal from anomalous scatterers including sulfur

Witek Kwiatkowski
The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the Cr K, radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the Cu K, and Cr K, data were similar but better than that for Au L,. This result was in spite of the fourfold higher flux from the Cu anode versus the Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the Cr K, data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the Au L, data. The ability to enhance the S-derived anomalous signal using Cr K, radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the Cr K, data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method. [source]

Overview and new developments in softer X-ray (2┼ < , < 5┼) protein crystallography

John R. Helliwell
New methodologies with synchrotron radiation and X-ray free electron lasers (XFELs) in structural biology are being developed. Recent trends in harnessing softer X-rays in protein crystallography for phase determination are described. These include reference to a data-collection test at 2.6 ┼ wavelength with a lysozyme crystal on SRS station 7.2 (Helliwell, 1983) and also use of softer X-rays (2,┼ wavelength) to optimise f," at the xenon L1 absorption edge in the Single Isomorphous Replacement Optimised Anomalous Scattering ('SIROAS') structure determination of apocrustacyanin A1 with four, partially occupied, xenon atoms (Cianci et al., 2001; Chayen et al., 2000). The hand of the protein was determined using the f," enhanced sulphur anomalous signal from six disulphides in the protein dimer of 40,kDa. In a follow-up study the single wavelength xenon L1 -edge f," optimised data set alone was used for phase determination and phase improvement by solvent flattening etc. (CCP4 DM) (Olczak et al., 2003). Auto-tracing of the protein was feasible but required additional diffraction data at higher resolution. This latter could be avoided in future by using improved tilted detector settings during use of softer X-rays, i.e. towards back-scattering recording (Helliwell, 2002). The Olczak et al. study has already led to optimisation of the new SRS beamline MPW,MAD,10 (see www.nwsgc.ac.uk) firstly involving the thinning of the beryllium windows as much as possible and planning for a MAR Research tilted detector `desk top beamline' geometry. Thus the use of softer, i.e. 2 to 3,┼ wavelength range, X-rays will allow optimisation of xenon and iodine L -edge f," and enhancing of sulphur f," signals for higher throughput protein crystallography. Softer X-rays utilisation in protein crystallography includes work done on SRS bending-magnet station 7.2 in the early 1980s by the author as station scientist (Helliwell, 1984). In the future development of XFELs these softer X-ray wavelengths could also be harnessed and relax the demands to some extent on the complexity and cost of an XFEL. Thus, by use of say 4,┼ XFEL radiation and use of a back-scattering geometry area detector the single molecule molecular transform could be sampled to a spatial resolution of 2,┼, sufficient, in principle, for protein model refinement (Miao et al., 1999). Meanwhile, Miao et al. (2003) report the first experimental recording of the diffraction pattern from intact Escherichia coli bacteria using coherent X-rays, with a wavelength of 2,┼, at a resolution of 30,nm and a real-space image constructed. The new single-particle X-ray diffraction-imaging era has commenced. [source]

New opportunities in biological and chemical crystallography

John R. Helliwell
Banerjee [Proc. R. Soc. (1933), 141, 188,193] offered a new way of approaching the crystallographic phase problem which not only broke new ground beyond the `trial and error' structure solution method of that time but also heralded the extremely powerful direct methods of crystallography of the modern era from the 1970s onwards in chemical crystallography. Some 200000 crystal structures are known today. More complex crystal structures such as proteins required new experimental and theoretical methods to solve the phase problem. These are still evolving, and new methods and results involving synchrotron radiation at softer X-ray wavelengths (2,┼) are reported. In addition, an overview is given of the new opportunities that are possible for biological and chemical crystallography, especially via harnessing synchrotron radiation and neutron beams. [source]