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Phasing
Kinds of Phasing Terms modified by Phasing Selected AbstractsPhasing Out Cadmium, Lead, and MercuryJOURNAL OF INDUSTRIAL ECOLOGY, Issue 1 2009Effects on Urban Stocks, Flows Summary Large stocks of metals have accumulated in the urban technosphere (i.e., the physical environment altered by human activity). To minimize health and environmental risks, attempts were begun in the 1980s to phase out the use of cadmium (Cd), lead (Pb), and mercury (Hg). To study the effect of this attempt, we conducted substance flow analyses (SFAs) in Stockholm, Sweden, in 1995 and in 2002,2003, which allow a comparison of the results over time. The SFAs showed a reduction in the stocks of Cd and Hg by approximately 25% to 30% between 1995 and 2002,2003. For Pb, the stock development was more uncertain. Cd and Hg inflow was substantially reduced during this period, but Pb inflow increased. Amounts of Cd and Pb in waste were still large, whereas Hg flows in waste were decreasing. Furthermore, although emissions of Pb decreased, Cd and Hg emissions were in the same range as in 1995. The application of SFAs has provided unique data on the accumulation of metals in the Stockholm technosphere, thus serving as a valuable indicator of how the phasing out progresses. The changes can be related to regulations, initiatives by industries and organizations, and the proactive attitude of the local environmental authorities and of the water company. [source] Purification, crystallization, X-ray diffraction analysis and phasing of a Fab fragment of monoclonal neuroantibody ,D11 against nerve growth factorACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2004Sonia Covaceuszach The rat monoclonal neuroantibody ,D11 is a potent antagonist that prevents the binding of nerve growth factor (NGF) to its tyrosine kinase A receptor (TrkA) in a variety of systems, most notably in two in vivo systems linked to crucial pathological states, such as Alzheimer's disease and HIV infection. To provide further insights into the mechanism of action of this potentially therapeutic monoclonal antibody, structural studies of the antigen-binding fragment (Fab) of ,D11 were performed. ,D11 IgG2a immunoglobulin was obtained from hybridomas by in vitro tissue culture. The ,D11 Fab crystallizes in two crystal forms. Form I belongs to space group P1, with unit-cell parameters a = 42.7, b = 50.6, c = 102.7,Å, , = 82.0, , = 89.1, , = 86.0°. With two molecules in the asymmetric unit, VM is 2.3,Å3,Da,1 and the solvent content is 46%. A complete data set has been collected at 2.7,Å resolution on beamline XRD-1 (ELETTRA, Trieste, Italy). Form II belongs to space group C2, with unit-cell parameters a = 114.8, b = 69.4, c = 64.10,Å, , = 117.0°. With one molecule in the asymmetric unit, VM is 2.4,Å3,Da,1 and the solvent content is 48%. A complete data set has been collected at 1.7,Å resolution on beamline ID14-1 (ESRF, Grenoble, France). Phasing was successfully performed by Patterson search techniques and refinement of the structures is currently under way. Crystal forms I and II display a close-packing pattern. [source] Gd-HPDO3A, a complex to obtain high-phasing-power heavy-atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozymeACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2002Éric Girard A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to use to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme were obtained by co-crystallization using different concentrations of the complex. Diffraction data from three derivative crystals (100, 50 and 10,mM) were collected to a resolution of 1.7,Å using Cu,K, radiation from a rotating anode. Two strong binding sites of the gadolinium complex to the protein were located from the gadolinium anomalous signal in both the 100 and 50,mM derivatives. A single site is occupied in the 10,mM derivative. Phasing using the anomalous signal at a single wavelength (SAD method) leads to an electron-density map of high quality. The structure of the 100,mM derivative has been refined. Two molecules of the gadolinium complex are close together. Both molecules are located close to tryptophan residues. Four chloride ions were found. The exceptional quality of the SAD electron-density map, only enhanced by solvent flattening, suggests that single-wavelength anomalous scattering with the Gd-HPDO3A complex may be sufficient to solve protein structures of high molecular weight by synchrotron-radiation experiments, if not by laboratory experiments. [source] Expression, crystallization and preliminary crystallographic analysis of SufE (XAC2355) from Xanthomonas axonopodis pv. citriACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2006Cristiane R. Guzzo Xanthomonas axonopodis pv. citri (Xac) SufE (XAC2355) is a member of a family of bacterial proteins that are conserved in several pathogens and phytopathogens. The Escherichia coli suf operon is involved in iron,sulfur cluster biosynthesis under iron-limitation and stress conditions. It has recently been demonstrated that SufE and SufS form a novel two-component cysteine desulfarase in which SufS catalyses the conversion of l -cysteine to l -alanine, forming a protein-bound persulfide intermediate. The S atom is then transferred to SufE, from which it is subsequently transferred to target molecules or reduced to sulfide in solution. Here, the cloning, expression, crystallization and phase determination of Xac SufE crystals are described. Recombinant SufE was crystallized in space group P212121 and diffracted to 1.9,Å resolution at a synchrotron source. The unit-cell parameters are a = 45.837, b = 58.507, c = 98.951,Å, , = , = , = 90°. The calculated Matthews coefficient indicated the presence of two molecules in the asymmetric unit. Phasing was performed by molecular-replacement using E. coli SufE as a model (PDB code 1mzg) and an interpretable map was obtained. [source] Crystallization, X-ray diffraction analysis and phasing of 17,-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2005Alberto Cassetta 17,-Hydroxysteroid dehydrogenase from the filamentous fungus Cochliobolus lunatus (17,-HSDcl) is an NADP(H)-dependent enzyme that preferentially catalyses the oxidoreduction of oestrogens and androgens. The enzyme belongs to the short-chain dehydrogenase/reductase superfamily and is the only fungal hydroxysteroid dehydrogenase known to date. 17,-HSDcl has recently been characterized and cloned and has been the subject of several functional studies. Although several hypotheses on the physiological role of 17,-HSDcl in fungal metabolism have been formulated, its function is still unclear. An X-ray crystallographic study has been undertaken and the optimal conditions for crystallization of 17,-HSDcl (apo form) were established, resulting in well shaped crystals that diffracted to 1.7,Å resolution. The space group was identified as I4122, with unit-cell parameters a = b = 67.14, c = 266.77,Å. Phasing was successfully performed by Patterson search techniques. A catalytic inactive mutant Tyr167Phe was also engineered, expressed, purified and crystallized for functional and structural studies. [source] Preliminary crystallographic analysis of the Escherichia coli YeaZ protein using the anomalous signal of a gadolinium derivativeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2005Richard Kahn The Escherichia coli yeaZ gene encodes a 231-residue protein (Mr = 25,180) that belongs to a family of proteins that are conserved in various bacterial genomes. This protein of unknown function is predicted to be a hypothetical protease. The YeaZ protein was overexpressed in E. coli and crystallized at 298,K by the hanging-drop vapour-diffusion method. A MAD data set was collected using a gadolinium-derivative crystal that had been soaked with 0.1,M Gd-DOTMA. The data set contained data collected to a resolution of 2.7,Å at two wavelengths at the LIII absorption edge of gadolinium, while remote data were collected to a resolution of 2.28,Å. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 76.3, b = 97.6, c = 141.9,Å. Phasing using the MAD method confirmed there to be four monomers in the asymmetric unit related by two twofold axes as identified by the self-rotation function search. [source] Spatial and temporal variation of passer Per2 gene expression in two distinct cell groups of the suprachiasmatic hypothalamus in the house sparrow (Passer domesticus)EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 3 2002Ute Abraham Abstract In mammals, the major pacemaker controlling circadian rhythmicity is located in the hypothalamic suprachiasmatic nuclei. Although there is evidence for the presence of a hypothalamic circadian oscillator in birds from lesioning studies, neuroanatomical, neurochemical and functional investigations have failed to identify its exact location. Two cell groups in the avian hypothalamus have been shown to bear characteristics of the mammalian suprachiasmatic nucleus: the suprachiasmatic nucleus and the lateral hypothalamic retinorecipient nucleus. We cloned an avian period homologue (pPer2) and investigated the temporal and spatial expression pattern of this gene in the house sparrow hypothalamus using in situ hybridization. Applying quantitative morphometry, we found rhythmic expression of pPer2 during light,dark as well as in constant conditions in the suprachiasmatic nucleus and in the lateral hypothalamus. The temporal and spatial distribution of pPer2 expression in the suprachiasmatic nucleus suggest a longitudinal compartmentalization of the nucleus with period gene expression being initiated in the most rostral portion of the suprachiasmatic nucleus before lights on. In the lateral hypothalamus, phasing of pPer2 -rhythmicity appeared different from the suprachiasmatic nucleus. The major difference between light,dark and constant conditions was a decrease in the amplitude of pPer2 rhythmicity in the suprachiasmatic nucleus. Our data demonstrate that, unlike in mammals, Per gene expression in the suprachiasmatic hypothalamus of the house sparrow is not confined to a single cell group, indicating a more complex organization of the circadian oscillator in the hypothalamus of birds. [source] Structure of Streptococcus agalactiae serine/threonine phosphataseFEBS JOURNAL, Issue 12 2007The subdomain conformation is coupled to the binding of a third metal ion We solved the crystal structure of Streptococcus agalactiae serine/threonine phosphatase (SaSTP) using a combination of single-wavelength anomalous dispersion phasing and molecular replacement. The overall structure resembles that of previously characterized members of the PPM/PP2C STP family. The asymmetric unit contains four monomers and we observed two novel conformations for the flap domain among them. In one of these conformations, the enzyme binds three metal ions, whereas in the other it binds only two. The three-metal ion structure also has the active site arginine in a novel conformation. The switch between the two- and three-metal ion structures appears to be binding of another monomer to the active site of STP, which promotes binding of the third metal ion. This interaction may mimic the binding of a product complex, especially since the motif binding to the active site contains a serine residue aligning remarkably well with the phosphate found in the human STP structure. [source] The polypeptide chain release factor eRF1 specifically contacts the s4UGA stop codon located in the A site of eukaryotic ribosomesFEBS JOURNAL, Issue 10 2001Laurent Chavatte It has been shown previously [Brown, C.M. & Tate, W.P. (1994) J. Biol. Chem.269, 33164,33170.] that the polypeptide chain release factor RF2 involved in translation termination in prokaryotes was able to photocrossreact with mini-messenger RNAs containing stop signals in which U was replaced by 4-thiouridine (s4U). Here, using the same strategy we have monitored photocrosslinking to eukaryotic ribosomal components of 14-mer mRNA in the presence of , and 42-mer mRNA in the presence of tRNAAsp (tRNAAsp gene transcript). We show that: (a) both 14-mer and 42-mer mRNAs crossreact with ribosomal RNA and ribosomal proteins. The patterns of the crosslinked ribosomal proteins are similar with both mRNAs and sensitive to ionic conditions; (b) the crosslinking patterns obtained with 42-mer mRNAs show characteristic modification upon addition of tRNAAsp providing evidence for appropriate mRNA phasing onto the ribosome. Similar changes are not detected with the 14-mer pairs; (c) when eukaryotic polypeptide chain release factor 1 (eRF1) is added to the ribosome·tRNAAsp complex it crossreacts with the 42-mer mRNA containing the s4UGA stop codon located in the A site, but not with the s4UCA sense codon; this crosslink involves the N-terminal and middle domains of eRF1 but not the C domain which interacts with eukaryotic polypeptide chain release factor 3 (eRF3); (d) addition of eRF3 has no effect on the yield of eRF1,42-mer mRNA crosslinking and eRF3 does not crossreact with 42-mer mRNA. These experiments delineate the in vitro conditions allowing optimal phasing of mRNA on the eukaryotic ribosome and demonstrate a direct and specific contact of ,core' eRF1 and s4UGA stop codon within the ribosomal A site. [source] Use of novel selenomethionine-resistant yeast to produce selenomethionyl protein suitable for structural analysisFEMS YEAST RESEARCH, Issue 3 2009Toshihiko Kitajima Abstract Yeast is widely used to determine the tertiary structure of eukaryotic proteins, because of its ability to undergo post-translational modifications such as glycosylation. A mutant lacking S -adenosylmethionine synthesis has been reported as a suitable host for producing selenomethionine derivatives, which can help solve phase problems in protein crystallography. However, the mutant required external addition of S -adenosylmethionine for cell proliferation. Here, a selenomethionine-resistant Pichia pastoris mutant that showed S -adenosylmethionine autotrophy was isolated. Human lysozyme expressed by the mutant under the control of constitutive promoter contained selenomethionine at 65% occupancy, sufficient for use as a selenomethionine derivative for single-wavelength anomalous dispersion phasing. [source] Energy efficiency improvement strategies for a diesel engine in low-temperature combustionINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 1 2009Ming Zheng Abstract The lowered combustion temperature in diesel engines is capable of reducing nitrogen oxides and soot simultaneously, which can be implemented by the heavy use of exhaust gas recirculation (EGR) or the homogeneous charge compression ignition (HCCI) type of combustion. However, the fuel efficiency of the low-temperature combustion (LTC) cycles is commonly compromised by the high levels of hydrocarbon and carbon monoxide emissions. More seriously, the scheduling of fuel delivery in HCCI engines has lesser leverage on the exact timing of auto-ignition that may even occur before the compression stroke is completed, which may cause excessive efficiency reduction and combustion roughness. New LTC control strategies have been explored experimentally to achieve ultralow emissions under independently controlled EGR, intake boost, exhaust backpressure, and multi-event fuel-injection events. Empirical comparisons have been made between the fuel efficiencies of LTC and conventional diesel cycles. Preliminary adaptive control strategies based on cylinder pressure characteristics have been implemented to enable and stabilize the LTC when heavy EGR is applied. The impact of heat-release phasing, duration, shaping, and splitting on the thermal efficiency has also been analyzed with engine cycle simulations. This research intends to identify the major parameters that affect diesel LTC engine thermal efficiency. Copyright © 2008 John Wiley & Sons, Ltd. [source] Autolabo: an automated system for ligand-soaking experiments with protein crystalsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2010Michihiro Sugahara Ligand soaking of protein crystals is important for the preparation of heavy-atom derivative crystals for experimental phasing as well as for large-scale ligand screening in pharmaceutical developments. To facilitate laborious large-scale ligand screening, to reduce the risk of human contact with hazardous ligand reagents and to increase the success rate of the soaking experiments, a protein crystallization robot `Autolabo' has been developed and implemented in the high-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center. The main functions of this robotic system are the production of protein crystals for experiments, the ligand soaking of these crystals and the observation of soaked crystals. The separate eight-channel dispensers of Autolabo eliminate the cross-contamination of reagents which should be strictly avoided in the ligand-soaking experiment. Furthermore, the automated approach reduces physical damage to crystals during experiments when compared with the conventional manual approach, and thereby has the potential to yield better quality diffraction data. Autolabo's performance as a ligand-soaking system was evaluated with a crystallization experiment on ten proteins from different sources and a heavy-atom derivatization experiment on three proteins using a versatile cryoprotectant containing heavy-atom reagents as ligands. The crystallization test confirmed reliable crystal reproduction in a single condition and the capability for crystallization with nucleants to improve crystal quality. Finally, Autolabo reproducibly derivatized the test protein crystals with sufficient diffraction quality for experimental phasing and model building, indicating a high potentiality of this automated approach in ligand-soaking experiments. [source] Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sitesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2009Xinguo Hong Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the program GASBOR at 5,Å resolution (qmax = 1.25,Å,1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8,Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2, level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax = 0.25,Å,1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination of FSEARCH and WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement. [source] The revenge of the Patterson methods.JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2007The Patterson techniques, recently developed by the same authors for the ab initio crystal structure solution of proteins, have been applied to single and multiple anomalous diffraction (SAD and MAD) data to find the substructure of the anomalous scatterers. An automatic procedure has been applied to a large set of test structures, some of which were originally solved with remarkable difficulty. In all cases, the procedure automatically leads to interpretable electron density maps. Patterson techniques have been compared with direct methods; the former seem to be more efficient than the latter, so confirming the results obtained for ab initio phasing, and disproving the common belief that they could only be applied to determine large equal-atom substructures with difficulty. [source] About the efficiency of the early FOMs in ab initio protein phasingJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2004Maria C. Burla All ab initio techniques for solving protein crystal structures use multisolution approaches. Several figures of merit that are found in the literature are efficient in the last steps of the phasing process, when some trials converge to the correct solution with a relatively small average phase error. Early figures of merit are much more critical; they should be able to recognize useful trials when the phase error is still large, and their efficiency determines the efficiency of the program. In the present work, a wide variety of known figures of merit at atomic and quasi-atomic (,1.4,Å) resolution have been tested; new figures have also been devised and tested. Their application to a large set of test structures allows the study of their properties at different data resolutions and the selection of the most efficient figures within the SIR2003-N framework. [source] Evaluation of SnB for the location of anomalous scattering atoms in SAD/MAD phasingJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2003Jun Wang Sixteen existing single-wavelength/multi-wavelength anomalous diffraction (SAD/MAD) data sets with a broad range of crystallographic properties have been used to investigate the various parameters in SnB with the goal of finding the optimum values for locating the positions of anomalous scatterers. The results of the analysis indicate some changes in default parameters that may be useful for non-routine and difficult cases. [source] Phasing Out Cadmium, Lead, and MercuryJOURNAL OF INDUSTRIAL ECOLOGY, Issue 1 2009Effects on Urban Stocks, Flows Summary Large stocks of metals have accumulated in the urban technosphere (i.e., the physical environment altered by human activity). To minimize health and environmental risks, attempts were begun in the 1980s to phase out the use of cadmium (Cd), lead (Pb), and mercury (Hg). To study the effect of this attempt, we conducted substance flow analyses (SFAs) in Stockholm, Sweden, in 1995 and in 2002,2003, which allow a comparison of the results over time. The SFAs showed a reduction in the stocks of Cd and Hg by approximately 25% to 30% between 1995 and 2002,2003. For Pb, the stock development was more uncertain. Cd and Hg inflow was substantially reduced during this period, but Pb inflow increased. Amounts of Cd and Pb in waste were still large, whereas Hg flows in waste were decreasing. Furthermore, although emissions of Pb decreased, Cd and Hg emissions were in the same range as in 1995. The application of SFAs has provided unique data on the accumulation of metals in the Stockholm technosphere, thus serving as a valuable indicator of how the phasing out progresses. The changes can be related to regulations, initiatives by industries and organizations, and the proactive attitude of the local environmental authorities and of the water company. [source] Applications of ACORN to data at 1.45 Å resolutionJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004V. Rajakannan One of the main interests in the molecular biosciences is in understanding structure,function relations and X-ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The , helices and , sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 Å (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 Å resolution and also to truncated data at 1.6 Å resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for `seed-phasing' to ACORN. [source] Reconstruction from a single diffraction pattern of azimuthally projected electron density of molecules aligned parallel to a single axisACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010D. K. Saldin Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. The limited size of the object results in continuous diffraction patterns characterized by neither Bragg spots nor layer lines. Equations relating the scattered amplitudes to the molecular electron density may be conveniently formulated in terms of cylindrical harmonics. For simulated diffraction patterns from short C nanotubes aligned along their axes, iterative solution of the equation for the zeroth-order cylindrical harmonic and its inverse with appropriate constraints in real and reciprocal space enables the phasing of the measured amplitudes, and hence a reconstruction of the azimuthal projection of the molecule. [source] An evolutionary computational approach to the phase problem in macromolecular X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2001Gordon Webster The ab initio computation of the molecular envelopes of two proteins exclusively from their corresponding diffraction amplitudes demonstrates that an efficient and inherently parallel evolutionary search algorithm can assist in the direct phasing of macromolecules for which almost no a priori structural information is available. The applicability of this evolutionary computational approach is general and should not be limited to the examples described nor to extremes of data resolution, symmetry or structural size. [source] Influence of the Madden,Julian Oscillation on East African rainfall.THE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 621 2006I: Intraseasonal variability, regional dependency Abstract The influence of the Madden,Julian Oscillation (MJO) on rainfall amounts over Equatorial East Africa (Kenya and northern Tanzania) is analysed for the period 1979,95 at the intraseasonal (pentad) time-scale. The two rainy seasons (March to May and October to December) are considered. Intraseasonal wet events in East Africa are embedded in large-scale zonal circulation anomaly patterns along the equator, showing distinct eastward propagation. It is further found that these ,wet' events display a clear phasing with respect to the MJO cycle. This phasing is expressed as out-of-phase variations between the Highland and the coastal areas. Such a pattern is suggested to reflect different rain-causing mechanisms. MJO phases leading to wet spells in the western (Highland) region are those associated with the development of large-scale convection in the Africa/Indian Ocean region. These events are unambiguously related to deep convection, fuelled by low-level westerly moisture advection. MJO phases leading to wet spells in the eastern (coastal) region are often those associated with overall suppressed deep convection in the Africa/Indian Ocean region. However, these phases induce moisture advection from Indian Ocean. The possible role of stratiform rainfall or relatively shallow convection in the coastal wet spells observed in this phase is discussed. The contrasting rainfall conditions found in the two regions for the two opposite MJO phases are strongly correlated with the pressure gradient between the Indian and Atlantic Oceans. Copyright © 2006 Royal Meteorological Society [source] The structure of the lunar semi-diurnal pressure tide L2THE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 606 2005Stephen W. Goulter Abstract The Hough structure of the lunar semi-diurnal tide L2(p) in surface pressure is estimated using joint weightings by area and probable-error structure, on annual and Lloyd seasonal scales, with new data. Global representations, on seasonal and annual scales of the L2 wave, in both spherical harmonic and Hough function forms, are presented for the Haurwitz,Cowley dataset enlarged by the more recent tidal determinations of Hutchings and Palumbo. These are mainly for southern hemiphere island locations. The asymmetric Hough eigenfunction terms H32 are considerably larger than previously estimated, both annually and seasonally, a possible artefact of the earlier data analysis technique. They are consistent and identified with the well-known difference in phasing and amplitude of L2 by hemisphere. The dependence of the Hough structure on the order of the fitting and on the more extreme residuals is examined. It is stable for the smallest models (spherical harmonic terms up to degree 6 and order 3), to removal of the largest residuals from a first fitting, and to the two largest datasets. Seasonal changes in the Hough structure are discussed. The asymmetric results appear consistent with early frictional/thermal interpretations on the seasonal variation of L2. But the sensitivity of L2 to upper-air temperature structure is not consistently shown in the analyses for the main mode H(2, 2). Copyright © 2005 Royal Meteorological Society. [source] FASTEX IOP 18: A very deep tropopause fold.THE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 577 2001I: Synoptic description, modelling Abstract The life cycle of a very deep tropopause fold (820 hPa) is documented with aircraft and ship observations during the Intensive Observing Period 18 of the Fronts and Atlantic Storm-Track EXperiment (FASTEX). The initial setting involves a coherent tropopause disturbance and an associated Arctic tropopause fold. The confluence episode that results from the phasing up of the tropopause disturbance and a southern ridge, ends in the formation of an intense jet streak, the dynamics of which are associated with the development of a polar tropopause fold. A diagnostic analysis suggests that the final dramatic stratospheric intrusion is the consequence of the vertical superposition of the Arctic and polar tropopause folds. The Mesoscale Non-Hydrostatic (Meso-NH) model is used to discuss this hypothesis. Mixing of the passive stratospheric tracer within the marine boundary layer is investigated with sensitivity tests which unplug, in turn, the model physical parametrizations. Finally, upper-level forcings associated with the development of the tropopause fold are investigated in detail in a companion paper. [source] 5-Amino-2,4,6-tribromoisophthalic acid: the MAD triangle for experimental phasingACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009Tobias Beck The title compound, C8H4Br3NO4, shows an extensive hydrogen-bond network. In the crystal structure, molecules are linked into chains by COO,H...O bonds, and pairs of chains are connected by additional COO,H...O bonds. This chain bundle shows stacking interactions and weak N,H...O hydrogen bonds with adjacent chain bundles. The three Br atoms present in the molecule form an equilateral triangle. This can be easily identified in the heavy-atom substructure when this compound is used as a heavy-atom derivative for experimental phasing of macromolecules. The title compound crystallizes as a nonmerohedral twin. [source] Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactionsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Radhika Malik The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2,Å resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg2+ and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH. [source] Structure of d -tyrosyl-tRNATyr deacylase using home-source Cu,K, and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme statesACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Manickam Yogavel d -Tyrosyl-tRNATyr deacylase (DTD) is an editing enzyme that removes d -amino acids from mischarged tRNAs. The crystal structure of Plasmodium falciparum DTD (PfDTD) was determined using the iodide-SAD phasing method. Iodide-derivatized PfDTD crystals were obtained using the quick cryo-soaking procedure in which native crystals were soaked for a short period of 10,30,s in cryoprotectant solution containing 0.2,1,M NaI. Iodide-SAD data sets were collected to 3.3 and 2.74,Å resolution from PfDTD crystals that belonged to two different space groups, P43 and P1, using an in-house X-ray copper-anode source. This is the first report to detail structure solution using low iodide anomalous signal, modest resolution and redundancy and average solvent content for SAD phasing of 984 and 1312 amino acids in the triclinic P1 and tetragonal P43 space groups, respectively. A total of 85% and 56% of the residues were automatically built into the iodide-phased electron-density maps using PHENIX AutoBuild. The structure of HEPES-bound PfDTD was subsequently determined by molecular replacement and refined to 2.83,Å resolution. The crystals obtained from various batches of crystallization trials of PfDTD exhibited polymorphism in terms of belonging to different crystal forms and space groups. Even within a given crystal system the unit-cell parameters showed high non-isomorphism. These packing variations were exploited in order to conduct a systematic study of conformational changes in PfDTD. It is shown that the disposition of a ten-residue insertion loop affects packing within the PfDTD crystals and seems to determine the non-isomorphism in unit-cell parameters. By tracking the changes in PfDTD unit cells, it was possible to map conformational differences within PfDTD that may be of significance for enzyme activity. [source] The magic triangle goes MAD: experimental phasing with a bromine derivativeACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Tobias Beck Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br,K edge was successfully carried out. Radiation damage to the bromine,carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out. [source] Carrying out an optimal experimentACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Zbigniew Dauter Diffraction data collection is the last experimental stage in structural crystallography. It has several technical and theoretical aspects and a compromise usually has to be found between various parameters in order to achieve optimal data quality. The influence and importance of various experimental parameters and their consequences are discussed in the context of different data applications, such as molecular replacement, anomalous phasing, high-resolution refinement or searching for ligands. [source] Experimental phasing: best practice and pitfallsACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Airlie J. McCoy Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real,imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods. [source] Experimental phasing with SHELXC/D/E: combining chain tracing with density modificationACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010George M. Sheldrick The programs SHELXC, SHELXD and SHELXE are designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXE by the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue ,-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a `no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap. [source] | ||||||||||||||||