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Neutron Data (neutron + data)
Selected AbstractsHigh-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2005I. Hazemann Neutron diffraction data have been collected to 2.2,Å resolution from a small (0.15,mm3) crystal of perdeuterated human aldose reductase (h-AR; MW = 36,kDa) in order to help to determine the protonation state of the enzyme. h-AR belongs to the aldo,keto reductase family and is implicated in diabetic complications. Its ternary complexes (h-AR,coenzyme NADPH,selected inhibitor) provide a good model to study both the enzymatic mechanism and inhibition. Here, the successful production of fully deuterated human aldose reductase [h-AR(D)], subsequent crystallization of the ternary complex h-AR(D),NADPH,IDD594 and neutron Laue data collection at the LADI instrument at ILL using a crystal volume of just 0.15,mm3 are reported. Neutron data were recorded to 2,Å resolution, with subsequent data analysis using data to 2.2,Å. This is the first fully deuterated enzyme of this size (36,kDa) to be solved by neutron diffraction and represents a milestone in the field, as the crystal volume is at least one order of magnitude smaller than those usually required for other high-resolution neutron structures determined to date. This illustrates the significant increase in the signal-to-noise ratio of data collected from perdeuterated crystals and demonstrates that good-quality neutron data can now be collected from more typical protein crystal volumes. Indeed, the signal-to-noise ratio is then dominated by other sources of instrument background, the nature of which is under investigation. This is important for the design of future instruments, which should take maximum advantage of the reduction in the intrinsic diffraction pattern background from fully deuterated samples. [source] Neutron Powder Diffraction Study of a Phase Transition in La0.68(Ti0.95Al0.05)O3JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 12 2006Roushown Ali Crystal structures and structural changes of the compound La0.68(Ti0.95Al0.05)O3 have been studied using neutron powder diffraction data and the Rietveld method in the temperature range from 25° to 592°C. The Rietveld profile-fitting analyses of the neutron data and the synchrotron diffraction profile revealed that the crystal symmetry of the low-temperature phase of La0.68(Ti0.95Al0.05)O3 is orthorhombic Cmmm (2ap× 2ap× 2ap; p: pseudo-cubic perovskite). The unit-cell and structural parameters were successfully refined with the orthorhombic Cmmm for the intensity data measured at 25°, 182°, and 286°C, and with the tetragonal P4/mmm (ap×ap× 2ap) for intensity data obtained at 388° and 592°C. The P4/mmm -to- Cmmm phase transition was found to be induced by tilting of the (TiAl)O6 octahedron. The tilt angle decreased with increasing temperature, reaching 0° at the Cmmm,P4/mmm transition temperature. [source] Towards the best model for H atoms in experimental charge-density refinementACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Anna A. Hoser The consequences of different treatments of H atoms in experimental charge-density studies are discussed. Geometric and topological parameters obtained after applying four different H-atom models in multipolar refinement on high-resolution X-ray data only were compared with the results obtained for a reference joint high-resolution X-ray/neutron refinement. The geometry and the topological critical point and integrated parameters closest to the reference values were obtained after a mixed refinement (high-order refinement of heavy atoms, low-angle refinement of H atoms and elongation of the X,H distance to the average neutron bond lengths) supplemented by an estimation of the anisotropic thermal motions of H atoms using the SHADE program. Such a procedure works very well even for strong hydrogen bonds. The worst fit to the reference results for both critical point and integrated parameters was obtained when only the standardization to the average neutron X,H distances was applied. The non-H-atom parameters are also systematically influenced by the H-atom modeling. In order to compare topological and integrated properties calculated for H and non-H atoms in multipolar refinement when there are no neutron data, the same treatment of H atoms (ideally the mixed refinement + estimated anisotropic atomic displacement parameters for H atoms) should be applied. [source] Solution of the crystallographic phase problem by iterated projectionsACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2003Veit Elser An algorithm for determining crystal structures from diffraction data is described which does not rely on the usual reciprocal-space formulations of atomicity. The new algorithm implements atomicity constraints in real space, as well as intensity constraints in reciprocal space, by projections that restore each constraint with the minimal modification of the scattering density. To recover the true density, the two projections are combined into a single operation, the difference map, which is iterated until the magnitude of the density modification becomes acceptably small. The resulting density, when acted upon by a single additional operation, is by construction a density that satisfies both intensity and atomicity constraints. Numerical experiments have yielded solutions for atomic resolution X-ray data sets with over 400 non-hydrogen atoms, as well as for neutron data, where positivity of the density cannot be invoked. [source] Magnetic behaviour of synthetic Co2SiO4ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Andrew Sazonov Synthetic Co2SiO4 crystallizes in the olivine structure (space group ) with two crystallographically non-equivalent Co positions and shows antiferromagnetic ordering below 50,K. We have investigated the temperature variation of the Co2SiO4 magnetic structure by means of non-polarized and polarized neutron diffraction for single crystals. Measurements with non-polarized neutrons were made at 2.5,K (below TN), whereas polarized neutron diffraction experiments were carried out at 70 and 150,K (above TN) in an external magnetic field of 7,T parallel to the b axis. Additional accurate non-polarized powder diffraction studies were performed in a broad temperature range from 5 to 500,K with small temperature increments. Detailed symmetry analysis of the Co2SiO4 magnetic structure shows that it corresponds to the magnetic (Shubnikov) group Pnma, which allows the antiferromagnetic configuration (Gx, Cy, Az) for the 4a site with inversion symmetry (Co1 position) and (0,Cy,0) for the 4c site with mirror symmetry m (Co2 position). The temperature dependence of the Co1 and Co2 magnetic moments obtained from neutron diffraction experiments was fitted in a modified molecular-field model. The polarized neutron study of the magnetization induced by an applied field shows a non-negligible amount of magnetic moment on the oxygen positions, indicating a delocalization of the magnetic moment from Co towards neighbouring O owing to superexchange coupling. The relative strength of the exchange interactions is discussed based on the non-polarized and polarized neutron data. [source] Towards a more reliable symmetry determination from powder diffraction: a redetermination of the low-temperature structure of 4-methylpyridine- N -oxideACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Palatinus The low-temperature structure of 4-methylpyridine- N -oxide was previously determined in symmetry P41 [Damay et al. (2006), Acta Cryst. B62, 627,633]. Using a recently published symmetry-determination method it was found that the true symmetry of the structure is P41212. The structure was refined in the new space group using X-ray and neutron data. The previously published structure is close to the newly refined structure, but the new structure is in agreement with the results of rotational tunneling spectroscopy, and, in contrast to the structure in symmetry P41, does not require a twofold degeneracy of the tunneling bands. [source] X-ray and neutron structure of 1,8-(3,6,9-trioxaundecane-1,11-diyldioxy)-9,10-dihydro-10,10-dimethylanthracene-9-ol (P326); some pitfalls of automatic data collectionACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Rex A. Palmer The structure of the crown ether 1,8-(3,6,9-trioxaundecane-1,11-diyldioxy)-9,10-dihydro-10,10-dimethylanthracene-9-ol, C24H30O6·H2O (1), code name P326, the parent compound for a series of derivatives, has been determined by both X-ray diffraction at room temperature and neutron diffraction at very low temperature. The unit cells are very similar at both temperatures and in both cases the crystals exhibit P21 symmetry with Z = 4 (two molecules, A and B, respectively, per asymmetric unit) and pseudosymmetry P21/c. The higher symmetry is broken mainly by the two independent water molecules in the unit cell, some reflections which would be absent in P21/c having strong intensities in both the X-ray and neutron data. In both molecules A and B hydrogen bonds involving the water molecule stabilize the macrocyclic ring structure, one involving the macrocyclic O(9) as a donor. Close contacts between the water and macrocyclic O atoms in each molecule also suggest the presence of two bifurcated hydrogen bonds, involving water HW2 to both O(16) and O(18), and water HW1 to both O(18) and O(20), respectively, with considerable variation in the geometry being present. Both molecules A and B exhibit very close pseudosymmetry across a plane perpendicular to the molecular plane and through atoms C(9) and O(18), and in addition are predominantly planar structures. The X-ray analysis failed to reveal one H atom per water molecule, each being subsequently included after location and refinement in the neutron analysis. [source] Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Anna S. Gardberg The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65,Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3 -protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1,Å resolution X-ray diffraction studies of the same protein at both RT and 100,K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the , level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65,Å resolution RT neutron data for perdeuterated rubredoxin are ,8 times more likely overall to provide high-confidence positions for D atoms than 1.1,Å resolution X-ray data at 100,K or RT. At or above the 1.0, level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1,Å resolution 100,K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0, level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only. [source] A neutron crystallographic analysis of T6 porcine insulin at 2.1,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2009Wakari Iwai Neutron diffraction data for T6 porcine insulin were collected to 2.1,Å resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structure was refined to a residual of 0.179. The hydrogen-bonding network of the central core of the hexamer was observed and the charge balance between positively charged Zn ions and their surrounding structure was interpreted by considering the protonation and/or deprotonation states and interactions of HisB10, water and GluB13. The observed double conformation of GluB13 was essential to interpreting the charge balance and could be compared with the structure of a dried crystal of T6 human insulin at 100,K. Differences in the dynamic behaviour of the water molecules coordinating the upper and lower Zn ions were observed and interpreted. The hydrogen bonds in the insulin molecules, as well as those involving HisB10 and GluB13, are discussed. The hydrogen/deuterium (H/D) exchange ratios of the amide H atoms of T6 porcine insulin in crystals were obtained and showed that regions highly protected from H/D exchange are concentrated in the centre of a helical region of the B chains. From the viewpoint of soaking time versus H/D-exchange ratios, the amide H atoms can be classified into three categories. [source] High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2005I. Hazemann Neutron diffraction data have been collected to 2.2,Å resolution from a small (0.15,mm3) crystal of perdeuterated human aldose reductase (h-AR; MW = 36,kDa) in order to help to determine the protonation state of the enzyme. h-AR belongs to the aldo,keto reductase family and is implicated in diabetic complications. Its ternary complexes (h-AR,coenzyme NADPH,selected inhibitor) provide a good model to study both the enzymatic mechanism and inhibition. Here, the successful production of fully deuterated human aldose reductase [h-AR(D)], subsequent crystallization of the ternary complex h-AR(D),NADPH,IDD594 and neutron Laue data collection at the LADI instrument at ILL using a crystal volume of just 0.15,mm3 are reported. Neutron data were recorded to 2,Å resolution, with subsequent data analysis using data to 2.2,Å. This is the first fully deuterated enzyme of this size (36,kDa) to be solved by neutron diffraction and represents a milestone in the field, as the crystal volume is at least one order of magnitude smaller than those usually required for other high-resolution neutron structures determined to date. This illustrates the significant increase in the signal-to-noise ratio of data collected from perdeuterated crystals and demonstrates that good-quality neutron data can now be collected from more typical protein crystal volumes. Indeed, the signal-to-noise ratio is then dominated by other sources of instrument background, the nature of which is under investigation. This is important for the design of future instruments, which should take maximum advantage of the reduction in the intrinsic diffraction pattern background from fully deuterated samples. [source] Preliminary joint neutron and X-ray crystallographic study of human carbonic anhydrase IIACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009S. Z. Fisher Carbonic anhydrases catalyze the interconversion of CO2 to HCO3,, with a subsequent proton-transfer (PT) step. PT proceeds via a proposed hydrogen-bonded water network in the active-site cavity that is stabilized by several hydrophilic residues. A joint X-ray and neutron crystallographic study has been initiated to determine the specific water network and the protonation states of the hydrophilic residues that coordinate it in human carbonic anhydrase II. Time-of-flight neutron crystallographic data have been collected from a large (,1.2,mm3) hydrogen/deuterium-exchanged crystal to 2.4,Å resolution and X-ray crystallographic data have been collected from a similar but smaller crystal to 1.5,Å resolution. Obtaining good-quality neutron data will contribute to the understanding of the catalytic mechanisms that utilize water networks for PT in protein environments. [source] | ||||||||||