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Diffraction Intensities (diffraction + intensity)
Selected AbstractsSpace-group determination from powder diffraction data: a probabilistic approachJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2004Angela Altomare Experimental powder diffraction diagrams, once indexed and decomposed into single diffraction intensities, can be submitted to statistical analysis for the determination of space-group symmetry. A new algorithm is illustrated, which is able to provide, on a quantitative basis, a probability value for each extinction symbol compatible with the previously established lattice symmetry. The algorithm has been implemented in EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst.37, 1025,1028] and has been successfully tested using a large set of experimental data. [source] Retrieving low- and medium-resolution structural features of macromolecules directly from the diffraction intensities , a real-space approach to the X-ray phase problemACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2008Wu-Pei Su A simple mathematical algorithm is proposed to generate electron-density functions whose Fourier amplitudes match the diffraction intensities. The function is by construction everywhere positive. Using appropriate averaging procedures, the high-density regions of such functions could yield important structural information about macromolecular crystals. Trial calculations on protein crystals show that the protein envelope plus other structural motifs such as barrels and secondary structures could be recognized in the density maps. As such, the algorithm could provide a basis for new phasing methods or supplement existing phasing methods. [source] Phase and amplitude recovery and diffraction image generation method: structure of Sb/Au(110),,3,×,,3R54.7° from surface X-ray diffractionACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2007R. Fung The discovery that the phase problem of diffraction from non-periodic objects may be solved by oversampling the diffraction intensities in reciprocal space with respect to a Nyquist criterion has opened up new vistas for structure determination by diffraction methods. A similar principle may be applied to the problem of surface X-ray diffraction (SXRD), where, owing to the breaking of a crystal periodicity normal to its surface, diffraction data consist of a set of superstructure rods (SRs) due to scattering from the parts of the surface whose structure is different from that of the truncated bulk and of crystal truncation rods (CTRs), formed by interfering contributions from the surface and the bulk. A phase and amplitude recovery and diffraction image generation method (PARADIGM) is described that provides a prescription for finding the unmeasured amplitudes and phases of the surface contributions to the CTRs in addition to the phases of the SRs, directly from the diffraction data. The resulting `diffraction image' is the basis of a determination of the previously unknown multidomain structure of Sb/Au(110),,3,×,,3R54.7°. [source] X-ray diffraction by a crystal in a permanent external electric field: general considerationsACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2005Semen V. Gorfman The variations of X-ray diffraction intensities from a crystal in the presence of a permanent external electric field is modeled analytically using a first-order stationary perturbation theory. The change in a crystal, induced by an external electric field, is separated into two contributions. The first one is related to a pure polarization of an electron subsystem, while the second contribution can be reduced to the displacements of the rigid pseudoatoms from their equilibrium positions. It is shown that a change of the X-ray diffraction intensities mainly originates from the second contribution, while the influence of the pure polarization of a crystal electron subsystem is negligibly small. The quantities restored from an X-ray diffraction experiment in the presence of an external electric field were analyzed in detail in terms of a rigid pseudoatomic model of electron density and harmonic approximation for the atomic thermal motion. Explicit relationships are derived that link the properties of phonon spectra with E -field-induced variations of a structure factor, pseudoatomic displacements and piezoelectric strains. The displacements can be numerically estimated using a model of independent atomic motion if the Debye,Waller factors and pseudoatomic charges are known either from a previous single-crystal X-ray diffraction study or from density functional theory calculations. The above estimations can be used to develop an optimum strategy for a data collection that avoids the measurements of reflections insensitive to the electric-field-induced variations. [source] Features of the electron density in magnesium diboride: reconstruction from X-ray diffraction data and comparison with TB-LMTO and FPLO calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2003S. Lee Features of the electron density in MgB2 reconstructed from room-temperature single-crystal X-ray diffraction intensities using a multipole model are considered. Topological analysis of the total electron density has been applied to characterize the atomic interactions in magnesium diboride. The shared-type B,B interaction in the B-atom layer reveals that both , and , components of the bonding are strong. A closed-shell-type weak B,B , interaction along the c axis of the unit cell has also been found. The Mg,B closed-shell interaction exhibits a bond path that is significantly curved towards the vertical Mg-atom chain ([110] direction). The latter two facts reflect two sorts of bonding interactions along the [001] direction. Integration of the electron density over the zero-flux atomic basins reveals a charge transfer of ,1.4,(1) electrons from the Mg atoms to the B-atom network. The calculated electric-field gradients at nuclear positions are in good agreement with experimental NMR values. The anharmonic displacement of the B atoms is also discussed. Calculations of the electron density by tight-binding linear muffin-tin orbital (TB-LMTO) and full-potential non-orthogonal local orbital (FPLO) methods confirm the results of the reconstruction from X-ray diffraction; for example, a charge transfer of 1.5 and 1.6 electrons, respectively, was found. [source] DIBER: protein, DNA or both?ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Grzegorz Chojnowski The program DIBER (an acronym for DNA and FIBER) requires only native diffraction data to predict whether a crystal contains protein, B-form DNA or both. In standalone mode, the classification is based on the cube root of the reciprocal unit-cell volume and the largest local average of diffraction intensities at 3.4,Å resolution. In combined mode, the Phaser rotation-function score (for the 3.4,Å shell and a canonical B-DNA search model) is also taken into account. In standalone (combined) mode, DIBER classifies 87.4 ± 0.2% (90.2 ± 0.3%) of protein, 69.1 ± 0.3% (78.8 ± 0.3%) of protein,DNA and 92.7 ± 0.2% (90.0 ± 0.2%) of DNA crystals correctly. Reliable predictions with a correct classification rate above 80% are possible for 36.8 ± 1.0% (60.2 ± 0.4%) of the protein, 43.6 ± 0.5% (59.8 ± 0.3%) of the protein,DNA and 83.3 ± 0.3% (82.6 ± 0.4%) of the DNA structures. Surprisingly, selective use of the diffraction data in the 3.4,Å shell improves the overall success rate of the combined-mode classification. An open-source CCP4/CCP4i -compatible version of DIBER is available from the authors' website at http://www.iimcb.gov.pl/diber and is subject to the GNU Public License. [source] De-icing: recovery of diffraction intensities in the presence of ice ringsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Michael S. Chapman Macromolecular structures are routinely determined at cryotemperatures using samples flash-cooled in the presence of cryoprotectants. However, sometimes the best diffraction is obtained under conditions where ice formation is not completely ablated, with the result that characteristic ice rings are superimposed on the macromolecular diffraction. In data processing, the reflections that are most affected by the ice rings are usually excluded. Here, an alternative approach of subtracting the ice diffraction is tested. High completeness can be retained with little adverse effect upon the quality of the integrated data. This offers an alternate strategy when high levels of cryoprotectant lead to loss of crystal quality. [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] Diffraction data analysis in the presence of radiation damageACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Dominika Borek In macromolecular crystallography, the acquisition of a complete set of diffraction intensities typically involves a high cumulative dose of X-ray radiation. In the process of data acquisition, the irradiated crystal lattice undergoes a broad range of chemical and physical changes. These result in the gradual decay of diffraction intensities, accompanied by changes in the macroscopic organization of crystal lattice order and by localized changes in electron density that, owing to complex radiation chemistry, are specific for a particular macromolecule. The decay of diffraction intensities is a well defined physical process that is fully correctable during scaling and merging analysis and therefore, while limiting the amount of diffraction, it has no other impact on phasing procedures. Specific chemical changes, which are variable even between different crystal forms of the same macromolecule, are more difficult to predict, describe and correct in data. Appearing during the process of data collection, they result in gradual changes in structure factors and therefore have profound consequences in phasing procedures. Examples of various combinations of radiation-induced changes are presented and various considerations pertinent to the determination of the best strategies for handling diffraction data analysis in representative situations are discussed. [source] Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1CACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Yingssu Tsai Lattice-translocation or crystal order,disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two layers of cyclic protein hexamers. The first layer is fully ordered (i.e. has one fixed position), while the second layer randomly takes one of three alternative positions whose displacements are related to each other by threefold symmetry. Remarkably, the highest symmetry present in the crystal is P3, yet the intensity data (and the Patterson map) obey 6/m instead of symmetry; the intensities exceed the symmetry expected from combining the crystal space group with an inversion center. The origin of this rare phenomenon, known as symmetry enhancement, is discussed and shown to be possible even for a perfectly ordered crystal. The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions. [source] Twinned crystals and anomalous phasingACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2003Zbigniew Dauter Merohedral or pseudomerohedral twinning of crystals cannot be identified from inspection of the diffraction patterns. Several methods for the identification of twinning and the estimation of the twin fraction are suitable for macromolecular crystals and all are based on the statistical properties of the measured diffraction intensities. If the crystal twin fraction is estimated and is not too close to 0.5, the diffraction data can be detwinned; that is, related to the individual crystal specimen. However, the detwinning procedure invariably introduces additional inaccuracies to the estimated intensities, which substantially increase when the twin fraction approaches 0.5. In some cases, a crystal structure can be solved with the original twinned data by standard techniques such as molecular replacement, multiple isomorphous replacement or multiwavelength anomalous diffraction. Test calculations on data collected from a twinned crystal of gpD, the bacteriophage , capsid protein, show that the single-wavelength anomalous diffraction (SAD) method can be used to solve its structure even if the data set corresponds to a perfectly twinned crystal with a twin fraction of 0.5. [source] Structure determination of adeno-associated virus 2: three complete virus particles per asymmetric unitACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2003Qing Xie The atomic structure of adeno-associated virus 2 (AAV-2) has been determined to 3.0,Å resolution. AAV-2 crystallized in space group P1, with unit-cell parameters a = 249.7, b = 249.7, c = 644.8,Å, , = 90.0, , = 101.2, , = 120.0°. The crystals contained three full virus particles in the asymmetric unit, allowing 180-fold non-crystallographic symmetry averaging. The particle orientations were determined using the self-rotation function and found to have similar but resolvably different orientations. Approximate alignment of icosahedral and interparticle threefold screw symmetry led to a native Patterson that was interpretable in terms of approximate particle positions. Accurate positions required a Patterson correlation search that was constrained to be consistent with non-crystallographic threefold projection symmetry evident in the diffraction intensities. Initial phases to 15.0,Å resolution were calculated by molecular replacement using the known structure of a distantly related homolog (23% sequence identity). Real-space averaging was performed and phases were extended from 15.0 to 3.0,Å. An atomic model was fitted and refined using a simulated-annealing real-space procedure. [source] Redetermination of the crystal structure of ,-copper phthalocyanine grown on KClACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2003Akitaka Hoshino The crystal structure of a polymorph of copper phthalocyanine (CuPc) grown on a KCl substrate is redetermined by transmission electron diffraction. It has a triclinic unit cell containing one molecule; the crystal does not have a herringbone-type molecular arrangement, which is a common packing mode of planar phthalocyanines. The molecular packing is determined by the diffraction intensity with the aid of the calculation of molecular packing energy. One of the striking features of this polymorph is its stacking mode within a molecular column: the molecular stacking direction projected on a molecular plane is different by an angle of about 45° from that of the ,-modifications of platinum phthalocyanine (PtPc) and metal-free phthalocyanine (H2Pc). A powder X-ray diffraction profile calculated for the polymorph agrees well with that of so-called ,-CuPc and Rietveld analysis for ,-CuPc indicates that the CuPc crystals grown on KCl are actually ,-CuPc; hence, ,-CuPc is not isostructural with either ,-PtPc or ,-H2Pc. On the basis of the present results and the reported crystal structures of the planar phthalocyanines that form molecular columns, the polymorphs of the phthalocyanines can be classified into four types distinguished by the molecular stacking mode within the column: ,(×)-, ,(+)-, ,(×)- and ,(+)-types. [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] | ||||||||||