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Diffracted Intensity (diffracted + intensity)
Selected AbstractsA comparison of a microfocus X-ray source and a conventional sealed tube for crystal structure determinationJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2009Thomas Schulz Experiments are described in which a direct comparison was made between a conventional 2,kW water-cooled sealed-tube X-ray source and a 30,W air-cooled microfocus source with focusing multilayer optics, using the same goniometer, detector, radiation (Mo,K,), crystals and software. The beam characteristics of the two sources were analyzed and the quality of the resulting data sets compared. The Incoatec Microfocus Source (IµS) gave a narrow approximately Gaussian-shaped primary beam profile, whereas the Bruker AXS sealed-tube source, equipped with a graphite monochromator and a monocapillary collimator, had a broader beam with an approximate intensity plateau. Both sources were mounted on the same Bruker D8 goniometer with a SMART APEX II CCD detector and Bruker Kryoflex low-temperature device. Switching between sources simply required changing the software zero setting of the 2, circle and could be performed in a few minutes, so it was possible to use the same crystal for both sources without changing its temperature or orientation. A representative cross section of compounds (organic, organometallic and salt) with and without heavy atoms was investigated. For each compound, two data sets, one from a small and one from a large crystal, were collected using each source. In another experiment, the data quality was compared for crystals of the same compound that had been chosen so that they had dimensions similar to the width of the beam. The data were processed and the structures refined using standard Bruker and SHELX software. The experiments show that the IµS gives superior data for small crystals whereas the diffracted intensities were comparable for the large crystals. Appropriate scaling is particularly important for the IµS data. [source] A standardless X-ray diffraction method for the quantitative analysis of multiphase mixtures.JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2002In 1987, Rius, Plana & Palanques [J. Appl. Cryst. (1987), 20, 457,460] devised an X-ray powder diffraction method based on the `least-squares' determination of calibration constants using only the diffracted intensities and the calculated absorption coefficients of the components. This method was developed for `infinitely thick' samples, a condition which is seldom met by airborne particulates because of the small amount of material normally available. Since the analysis of such samples may become one of the principal applications of the method, this condition represents a serious limitation. The simplest way to overcome this limitation is by correcting the measured intensities. This can be done either by direct measurement of the sample transmission, or alternatively, by using refined transmission values. In the latter case no experimental values are necessary. With the help of some test calculations, the viability of both possibilities has been explored. [source] Radiation-induced site-specific damage of mercury derivatives: phasing and implicationsACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2005Udupi A. Ramagopal The behavior of mercury-derivatized triclinic crystals of a 60,kDa protein target from the New York Structural GenomiX Research Consortium provides novel insights into the mechanism of heavy-atom-specific radiation damage and its potential exploitation for de novo structure solution. Despite significant anomalous signal, structure solution by classic SAD and MAD phasing approaches was not successful. A detailed analysis revealed that significant isomorphic variation of the diffracted intensities was induced by X-ray irradiation. These intensity changes allowed the crystal structure to be solved by the radiation-damage-induced phasing (RIP) technique. Inspection of the crystal structure and electron-density maps demonstrated that the covalent S,Hg bonds at all four derivatized cysteine sites were much more susceptible to radiation-induced cleavage than other bonds typically present in native proteins. A simple diagnostic is described to identify the fingerprint of such decay at the time of data collection/processing. The rapid radiation-induced decomposition of mercury adducts is consistent with the difficulties frequently associated with the experimental phasing of mercury derivatives and suggests a straightforward solution to overcome this limitation by radiation-damage-induced phasing with anomalous scattering (RIPAS). These results indicate that historically recalcitrant and newly emerging difficulties associated with Hg phasing should be revisited. [source] Cold pressing of copper single crystals for a large-area doubly focusing monochromatorJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2004D. F. R. Mildner The design for a large-area doubly focusing neutron monochromator consists of a large number of small square copper single crystals mounted onto thin aluminium blades that both buckle and rotate independently. This avoids the need for large individual alignment mechanisms for each crystal that introduce unacceptably high levels of background. However, it does require that the crystals be oriented such that the diffracting crystallographic planes are parallel to the crystal face. Cold pressing broadens the natural narrow mosaic of the virgin crystal discs to increase the diffracted intensity. This introduces anisotropy into the crystal that determines its orientation in the final monochromator. The alignment procedure used for each crystal before cutting out the square tile in the correct orientation is described. A few crystals are characterized in detail by neutron diffraction at various stages of the operation, revealing the variation in the mosaic width and the angular position of the reciprocal-lattice vector as a function of the azimuthal angle by rotating the crystal about the normal to its face. The twofold symmetry of the mosaic width of the pressed crystal is modulated by the 2, periodicity introduced by the precession of the reciprocal-lattice vector around the crystal face normal. Satisfactorily aligned crystals have a variation in the angular position for diffraction within the allowed tolerance. [source] X-ray diffraction from inhomogeneous thin films of nanometre thickness: modelling and experimentJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2003F. Bocquet The diffraction of X-rays by a thin layer (of the order of a few nanometres) with a gradient in interplanar spacings is considered. It is shown that optical coherence over the film thickness leads to diffraction peak positions that no longer obey Bragg's law. Although a fitting of the diffracted intensity is indeed still possible, this has direct consequences on the applicability of more straightforward analysis methods, such as the sin2, method, which rely on diffraction peak positions. The intensity and peak position calculations are supported by a comparison with experimental data from a (001) Fe/GaAs thin (3,nm) epitaxic film. [source] Dynamical diffraction of ultrashort X-ray free-electron laser pulsesJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2001S. D. Shastri Calculations are presented for the femtosecond time-evolution of intensities of beams diffracted by perfect Bragg crystals illuminated with radiation expected from X-ray free-electron lasers (XFELs) operating through the self-amplified spontaneous emission (SASE) process. After examining the case of transient diffraction of an electromagnetic delta-function impulse through flat, single- and double-crystal monochromators, the propagation of a 280,fs-duration SASE XFEL pulse of 8,keV photons through the same optics is discussed. The alteration of the sub-femtosecond spiky microbunched temporal structure of the XFEL pulse after it passes through the system is shown for both low-order (broad bandwidth) and high-order (narrow bandwidth) crystal reflections. Finally, the shot-to-shot statistical fluctuations of the integrated diffracted intensity is simulated. Implications of these results for XFEL applications are addressed. [source] Phase modulation effects in X-ray diffraction from a highly deformed crystal with variable strain gradientACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2009M. Shevchenko The X-ray interbranch scattering by lattice distortions is studied for a thin crystal whose thickness is appreciably less than the conventional X-ray extinction length. The concept of interbranch phase modulation of the X-ray wavefield is extended to the case of a large gradient which depends on depth inside the crystal. The prominent interbranch features of the diffracted intensity are also established within this concept. Numerical calculations of the diffracted intensity are presented for an exponential strain gradient model to illustrate this. Diffraction (extinction) contrast is discussed for a strongly deformed specimen containing a single dislocation. It is predicted that for large values of the X-ray extinction length the extinction contrast may arise even in the case of a very thin crystal. This effect, owing to the interbranch phase changes of the waves scattered in the deformed matrix, is observed in experiments with protein crystals. [source] Know your dose: RADDOSEACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Karthik S. Paithankar The program RADDOSE is widely used to compute the dose absorbed by a macromolecular crystal during an X-ray diffraction experiment. A number of factors affect the absorbed dose, including the incident X-ray flux density, the photon energy and the composition of the macromolecule and of the buffer in the crystal. An experimental dose limit for macromolecular crystallography (MX) of 30,MGy at 100,K has been reported, beyond which the biological information obtained may be compromised. Thus, for the planning of an optimized diffraction experiment the estimation of dose has become an additional tool. A number of approximations were made in the original version of RADDOSE. Recently, the code has been modified in order to take into account fluorescent X-ray escape from the crystal (version 2) and the inclusion of incoherent (Compton) scattering into the dose calculation is now reported (version 3). The Compton cross-section, although negligible at the energies currently commonly used in MX, should be considered in dose calculations for incident energies above 20,keV. Calculations using version 3 of RADDOSE reinforce previous studies that predict a reduction in the absorbed dose when data are collected at higher energies compared with data collected at 12.4,keV. Hence, a longer irradiation lifetime for the sample can be achieved at these higher energies but this is at the cost of lower diffraction intensities. The parameter `diffraction-dose efficiency', which is the diffracted intensity per absorbed dose, is revisited in an attempt to investigate the benefits and pitfalls of data collection using higher and lower energy radiation, particularly for thin crystals. [source] Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicityACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2005Shinya Saijo A novel method has been developed to improve protein-crystal perfection during crystallization in a high magnetic field and structural studies have been undertaken. The three-dimensional structure of orthorhombic hen egg-white (HEW) lysozyme crystals grown in a homogeneous and static magnetic field of 10,T has been determined and refined to a resolution of 1.13,Å and an R factor of 17.0%. The 10,T crystals belonged to space group P212121, with unit-cell parameters a = 56.54,(3), b = 73.86,(6), c = 30.50,(2),Å and one molecule per asymmetric unit. A comparison of the structures of the 0,T and 10,T crystals has been carried out. The magnitude of the structural changes, with a root-mean-square deviation value of 0.75,Å for the positions of all protein atoms, is similar to that observed when an identical protein structure is resolved in two different crystalline lattices. The structures remain similar, with the exception of a few residues e.g. Arg68, Arg73, Arg128 and Gln121. The shifts of the arginine residues result in very significant structural fluctuations, which can have large effects on a protein's crystallization properties. The high magnetic field contributed to an improvement in diffraction intensity by (i) the displacement of the charged side chains of Arg68 and Arg73 in the flexible loop and of Arg128 at the C-terminus and (ii) the removal of the alternate conformations of the charged side chains of Arg21, Lys97 or Arg114. The improvement in crystal perfection might arise from the magnetic effect on molecular orientation without structural change and differences in molecular interactions. X-ray diffraction and molecular-modelling studies of lysozyme crystals grown in a 10,T field have indicated that the field contributes to the stability of the dihedral angle. The average difference in conformational energy has a value of ,578,kJ,mol,1 per charged residue in favour of the crystal grown in the magnetic field. For most protein atoms, the average B factor in the 10,T crystal shows an improvement of 1.8,Å2 over that for the 0,T control; subsequently, the difference in diffraction intensity between the 10,T and 0,T crystals corresponds to an increase of 22.6% at the resolution limit. The mosaicity of the 10,T crystal was better than that of the 0,T crystal. More highly isotropic values of 0.0065, 0.0049 and 0.0048° were recorded along the a, b and c axes, respectively. Anisotropic mosaicity analysis indicated that crystal growth is most perfect in the direction that corresponds to the favoured growth direction of the crystal, and that the crystal grown in the magnetic field had domains that were three times the volume of those of the control crystal. Overall, the magnetic field has improved the quality of these crystals and the diffracted intensity has increased significantly with the magnetic field, leading to a higher resolution. [source] | ||||||||||