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Maximum Resolution (maximum + resolution)
Selected AbstractsIncreasing the vertical resolution of conventional sub-bottom profilers by parametric equalizationGEOPHYSICAL PROSPECTING, Issue 2 2002P. Cobo ABSTRACT Vertical resolution, i.e. the ability to resolve two close reflectors, is a crucial aspect of pulses used in geo-acoustic exploration of sea sub-bottoms. This paper deals with the problem of exploring the shallowest unconsolidated layers of the seafloor with conventional piezo-electric sonar pulses. Such transducers do not have a sufficiently broad transmission response to enable them to radiate short high-resolution pulses. Therefore, some kind of equalization process must be applied to broaden the transmission response. Here, inverse filtering is used to calculate the transducer driving waveform so that the subsequent acoustic pulse has a zero-phase cosine-magnitude nature. Within a specified bandwidth, this pulse has minimum length, i.e. maximum resolution. The method has been applied to compress the acoustic pulses radiated by two piezo-electric transducers. In conventional performance, these transducers radiate narrowband pulses which contain several cycles at the natural resonance frequency. Under equalized driving, both transducers emit broadband pulses, with resolving power greatly increased, at the cost of some amplitude loss. That is, the pulses radiated by both transducers have been shortened from 1 ms (low-frequency transducer) and 0.274 ms (high-frequency transducer) in conventional performance to 0.13 ms and 0.038 ms in equalized mode, with amplitude losses of 33% and 56%, respectively. The great improvement in the resolution of this technique is demonstrated by comparing the synthetic echograms that should be obtained when exploring a wedge model using zero-phase cosine-magnitude pulses with conventional ping pulses. [source] On the tetragonality of the room-temperature ferroelectric phase of barium titanate, BaTiO3JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2009Dean S. Keeble The room-temperature phase of the important ferroelectric material barium titanate, BaTiO3, was re-investigated by single-crystal X-ray diffraction on a sample grown by the top-seeded solution growth method, with the intention of demonstrating once again that the structure has tetragonal symmetry consistent with the space-group assignment P4mm and thus resolving recent controversy in the scientific community and literature [Yoshimura, Kojima, Tokunaga, Tozaki & Koganezawa (2006). Phys. Lett. A, 353, 250,254; Yoshimura, Morioka, Kojima, Tokunaga, Koganezawa & Tozaki (2007). Phys. Lett. A, 367, 394,401]. To this end, the X-ray diffraction pattern of a small (341,µm3) sample of top-seeded solution-grown BaTiO3 was measured using an Oxford Diffraction Gemini CCD diffractometer employing Mo,K, radiation and an extended 120,mm sample-to-detector distance. More than 104 individual diffraction maxima observed out to a maximum resolution of 0.4,Å were indexed on two tetragonal lattices. These were identical to within the standard deviations on the lattice parameters and were related to each other by a single rotation of 119.7° about the [11] direction of the first tetragonal lattice (the major twin component), although the actual twinning operation that explains the observed diffraction pattern both qualitatively and quantitatively is shown to be conventional 90° twinning by the m[101] operation. Importantly, it is not necessary to invoke either monoclinic symmetry or a coexistence of tetragonal and monoclinic phases to explain the observed diffraction data. [source] A RAPID METHOD OF QUANTIFYING THE RESOLUTION LIMITS OF HEAT-FLOW ESTIMATES IN BASIN MODELSJOURNAL OF PETROLEUM GEOLOGY, Issue 2 2008A. Beha Deterministic forward models are commonly used to quantify the processes accompanying basin evolution. Here, we describe a workflow for the rapid calibration of palaeo heat-flow behaviour. The method determines the heat-flow history which best matches the observed data, such as vitrinite reflectance, which is used to indicate the thermal maturity of a sedimentary rock. A limiting factor in determining the heat-flow history is the ability of the algorithm used in the software for the maturity calculation to resolve information inherent in the measured data. Thermal maturation is controlled by the temperature gradient in the basin over time and is therefore greatly affected by maximum burial depth. Calibration, i.e. finding the thermal history model which best fits the observed data (e.g. vitrinite reflectance), can be a time-consuming exercise. To shorten this process, a simple pseudo-inverse model is used to convert the complex thermal behaviour obtained from a basin simulator into more simple behaviour, using a relatively simple equation. By comparing the calculated "simple" maturation trend with the observed data points using the suggested workflow, it becomes relatively straightforward to evaluate the range within which a best-fit model will be found. Reverse mapping from the simple model to the complex behaviour results in precise values for the heat-flow which can then be applied to the basin model. The goodness-of-fit between the modelled and observed data can be represented by the Mean Squared Residual (MSR) during the calibration process. This parameter shows the mean squared difference between all measured data and the respective predicted maturities. A minimum MSR value indicates the "best fit". Case studies are presented of two wells in the Horn Graben, Danish North Sea. In both wells calibrating the basin model using a constant heat-flow over time is not justified, and a more complex thermal history must be considered. The pseudo-inverse method was therefore applied iteratively to investigate more complex heat-flow histories. Neither in the observed maturity data nor in the recorded stratigraphy was there evidence for erosion which would have influenced the present-day thermal maturity pattern, and heat-flow and time were therefore the only variables investigated. The aim was to determine the simplest "best-fit" heat-flow history which could be resolved at the maximum resolution given by the measured maturity data. The conclusion was that basin models in which the predicted maturity of sedimentary rocks is calibrated solely against observed vitrinite reflectance data cannot provide information on the timing of anomalies in the heat-flow history. The pseudo inverse method, however, allowed the simplest heat-flow history that best fits the observed data to be found. [source] Structure determination using poorly diffracting membrane-protein crystals: the H+ -ATPase and Na+,K+ -ATPase case historyACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Bjørn P. Pedersen An approach is presented for the structure determination of membrane proteins on the basis of poorly diffracting crystals which exploits molecular replacement for heavy-atom site identification at 6,9,Å maximum resolution and improvement of the heavy-atom-derived phases by multi-crystal averaging using quasi-isomorphous data sets. The multi-crystal averaging procedure allows real-space density averaging followed by phase combination between non-isomorphous native data sets to exploit crystal-to-crystal nonisomorphism despite the crystals belonging to the same space group. This approach has been used in the structure determination of H+ -ATPase and Na+,K+ -ATPase using Ca2+ -ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated. [source] Towards the crystal structure of glycerol dehydrogenase from Thermotoga maritimaACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2002Vasundara Srinivasan The NAD+ -dependent glycerol dehydrogenase (EC 1.1.1.6) from the extremely thermophilic bacterium Thermotoga maritima has been crystallized in the presence of glycerol by the hanging-drop vapour-diffusion method using 2-methyl-2,4-pentanediol (MPD) as the precipitating agent. Crystals of the enzyme complexed with NAD+ have also been obtained. The crystals belong to the tetragonal system with space group I422 and unit-cell parameters a = 105.3, c = 134.5,Å. They diffract to a maximum resolution of 1.4,Å using synchrotron radiation (, = 0.838,Å). Crystals of the enzyme,NAD+ complex diffract to 2.5,Å resolution using in-house Cu,K, radiation. [source] Crystallization and preliminary crystallographic analysis of N -acetylglucosamine 6-phosphate deacetylase from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2000F. M. Ferreira N -Acetylglucosamine 6-phosphate deacetylase (E.C. 3.5.1.25), an enzyme from Escherichia coli involved in aminosugar catabolism, has been crystallized by the vapour-diffusion technique using phosphate as precipitant. X-ray diffraction experiments show the crystals to belong to the orthorhombic crystal system, with space group P21212. The unit-cell parameters are a = 82.09,(2), b = 114.50,(1), c = 80.17,(1),Å. The crystals diffract to a maximum resolution of 1.8,Å and an initial data set was collected to 2.0,Å. [source] Improved crystals of Thermus thermophilus prolyl-tRNA synthetase complexed with cognate tRNA obtained by crystallization from precipitateACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2000Anna Yaremchuk The complex between Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) and its cognate tRNA has been crystallized using two different isoacceptors of tRNAPro. Similar bipyramidal crystals of the complexes of ProRSTT with the two different tRNAPro isoacceptors grow within two weeks from 32% saturated ammonium sulfate solution. They belong to space group P43212, with unit-cell parameters a = 143.1, b = 143.1, c = 228.6,Å. The crystals diffract weakly to a maximum resolution of 3.1,Å. Superior quality crystals were obtained by growing slowly from precipitate over 5,6 months. These are of the same space group but have slightly altered unit-cell parameters, a = 140.8, b = 140.8, c = 237.0,Å. These crystals diffract more strongly to at least 2.8,Å resolution and a complete data set to 2.85,Å resolution has been collected from a single crystal. Comparison of the packing in the two crystal forms shows that domain flexibility contributes to the presence of different crystal contacts in the two forms. [source] Crystallization and preliminary X-ray diffraction analysis of rat autotaxinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Jacqueline E. Day Rat autotaxin has been cloned, expressed, purified to homogeneity and crystallized via hanging-drop vapour diffusion using PEG 3350 as precipitant and ammonium iodide and sodium thiocyanate as salts. The crystals diffracted to a maximum resolution of 2.05,Å and belonged to space group P1, with unit-cell parameters a = 53.8, b = 63.3, c = 70.5,Å, , = 98.8, , = 106.2, , = 99.8°. Preliminary X-ray diffraction analysis indicated the presence of one molecule per asymmetric unit, with a solvent content of 47%. [source] Purification, crystallization and preliminary X-ray analysis of apo glyceraldehyde-3-phosphate dehydrogenase 1 (GAP1) from methicillin-resistant Staphylococcus aureus (MRSA252)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Somnath Mukherjee Glyceraldehyde-3-phosphate dehydrogenase 1 (GAP1) from methicillin-resistant Staphylococcus aureus (MRSA252) has been purified to homogeneity in the apo form. The protein was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group P21, with unit-cell parameters a = 69.95, b = 93.68, c = 89.05,Å, , = 106.84°. X-ray diffraction data have been collected and processed to a maximum resolution of 2.2,Å. The presence of one tetramer in the asymmetric unit gives a Matthews coefficient (VM) of 1.81,Å3,Da,1 with a solvent content of 32%. The structure has been solved by molecular replacement and structure refinement is now in progress. [source] Crystallization and preliminary X-ray crystallographic analysis of the [NiFe]-hydrogenase maturation factor HypF1 from Ralstonia eutropha H16ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Gordon Winter The hydrogenase maturation factor HypF1 is a truncated but functional version of the HypF protein. HypF is known to be involved in the supply of the CN, ligands of the active site of [NiFe]-hydrogenases, utilizing carbamoyl phosphate as a substrate. The first crystallization and preliminary X-ray studies of HypF1 from Ralstonia eutropha H16 are reported here. Crystals of HypF1 (394 amino acids, 40.7,kDa) were obtained by the sitting-drop vapour-diffusion technique using sodium formate as a precipitant. The crystals belonged to space group I222, with unit-cell parameters a = 79.7, b = 91.6, c = 107.2,Å. Complete X-ray diffraction data sets were collected at 100,K from native crystals and from a platinum derivative to a maximum resolution of 1.65,Å. [source] Crystallization and preliminary X-ray diffraction studies of the carbohydrate-recognition domain of SIGN-R1, a receptor for microbial polysaccharides and sialylated antibody on splenic marginal zone macrophagesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Noella Silva-Martin SIGN-R1, or CD209b, is a mouse C-type lectin receptor that is expressed at high levels on macrophages in lymphoid tissues, especially within the marginal zone of the spleen. SIGN-R1 can bind and mediate the uptake of various microbial polysaccharides, including dextrans, lipopolysaccharides and pneumococcal capsular polysaccharides. It has been shown that SIGN-R1 mediates the clearance of encapsulated pneumococcus, complement fixation via binding C1q independent of antibody and innate resistance to pneumococcal infection. Recently, SIGN-R1 has also been demonstrated to bind sialylated antibody and mediate its activity to suppress autoimmunity. The carbohydrate-recognition domain (CRD) of SIGN-R1 has been cloned and overexpressed in a soluble secretory form in mammalian Chinese hamster ovary (CHO) cells. The CRD protein of SIGN-R1 was purified from CHO cell-culture supernatant and concentrated for crystallization using the hanging-drop vapour-diffusion method at 291,K. Crystals grew from a mixture of 2,M ammonium sulfate in 0.1,M bis-tris pH 5.5. Single crystals, which belonged to the monoclinic space group C2 with unit-cell parameters a = 146.72, b = 92.77, c = 77.06,Å, , = 121.66°, allowed the collection of a full X-ray data set to a maximum resolution of 1.87,Å. [source] Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Antheraea mylittaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Somnath Mukherjee Glyceraldehyde-3-phosphate dehydrogenase from Antheraea mylitta (AmGAPDH) was cloned in pQE30 vector, overexpressed in Escherichia coli M15 (pREP4) cells and purified to homogeneity. The protein was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group I222, with unit-cell parameters a = 85.81, b = 133.72, c = 220.37,Å. X-ray diffraction data were collected and processed to a maximum resolution of 2.2,Å. The presence of three molecules in the asymmetric unit gave a Matthews coefficient (VM) of 2.80,Å3,Da,1, with a solvent content of 56.08%. [source] A crystallizable form of the Streptococcus gordonii surface antigen SspB C-domain obtained by limited proteolysisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Nina Forsgren SspB is a 1500-residue adhesin expressed on the surface of the oral bacterium Streptococcus gordonii. Its interaction with other bacteria and host cells initiates the development of dental plaque. The full-length C-terminal domain of SspB was cloned, overexpressed in Escherichia coli and purified. However, the protein could not be crystallized. Limited proteolysis of the full-length C-domain identified a core fragment. The proteolysis product was cloned, expressed and purified. The protein was crystallized using the hanging-drop vapour-diffusion method. X-ray data were collected and processed to a maximum resolution of 2.1,Å with 96.4% completeness. The crystals belonged to space group P21, with one molecule in the asymmetric unit, a solvent content of 33.7% and a corresponding Matthews coefficient of 1.85,Å3,Da,1. [source] Expression, purification, crystallization and preliminary X-ray diffraction studies of triosephosphate isomerase from methicillin-resistant Staphylococcus aureus (MRSA252)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Somnath Mukherjee Triosephosphate isomerase from methicillin-resistant Staphylococcus aureus (MRSA252) was cloned in pQE30 vector, overexpressed in Escherichia coli M15 (pREP4) cells and purified to homogeneity. The protein was crystallized from 1.6,M trisodium citrate dihydrate pH 6.5 using the hanging-drop vapour-diffusion method. The crystals belonged to space group P43212, with unit-cell parameters a = b = 79.15, c = 174.27,Å. X-ray diffraction data were collected and processed to a maximum resolution of 1.9,Å. The presence of two molecules in the asymmetric unit gave a Matthews coefficient (VM) of 2.64,Å3,Da,1, with a solvent content of 53.63%. [source] Expression, purification, crystallization and preliminary X-ray diffraction analysis of the soluble domain of PPA0092, a putative nitrite reductase from Propionibacterium acnesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Masaki Nojiri The soluble domain (residues 483,913) of PPA0092, a putative copper-containing nitrite reductase from Propionibacterium acnes KPA171202, has been overexpressed in Escherichia coli. The purified recombinant protein was crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected and processed to a maximum resolution of 2.4,Å. The crystal belonged to space group P213, with unit-cell parameters a = b = c = 108.63,Å. Preliminary diffraction data show that one molecule is present in the asymmetric unit; this corresponds to a VM of 2.1,Å3,Da,1. [source] Crystallization and X-ray diffraction analysis of the RNA primer/promoter-binding domain of influenza A virus RNA-dependent RNA polymerase PB2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Takashi Kuzuhara The C-terminal domain protein (amino-acid residues 535,759) of the PB2 subunit of the RNA-dependent RNA polymerase from the highly pathogenic influenza A virus was expressed as a soluble protein in Escherichia coli and crystallized using sodium formate as a precipitant. Data sets were collected from crystals of native and selenomethionine-substituted protein on the KEK NW12 beamline at the Photon Factory and the crystals diffracted to a maximum resolution of 2.44,Å for the SeMet-derivative crystal. The native crystals were found to belong to space group P3221, with unit-cell parameters a = b = 52.5, c = 156.3,Å. The Matthews value (VM) was 2.7,Å3,Da,1, assuming the presence of one molecule in the asymmetric unit. The SeMet-derivative crystals were found to belong to the same space group, with unit-cell parameters a = b = 52.6, c = 156.4,Å. Attempts are being made to solve the structure by multi-wavelength anomalous dispersion phasing. [source] Expression, purification, crystallization and preliminary X-ray diffraction analysis of the transcriptional repressor SirR from Mycobacterium tuberculosis H37RvACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Baisakhee Saha SirR, a metal-dependent transcriptional repressor from Mycobacterium tuberculosis (Rv2788), was cloned in pQE30 expression vector with an N-terminal His6 tag for heterologous overexpression in Escherichia coli M15 (pREP4) cells and purified to homogeneity using chromatographic procedures. The purified protein was crystallized using the sitting-drop vapour-diffusion technique. The crystals belonged to the tetragonal space group P41212/P43212, with unit-cell parameters a = 105.21, b = 105.21, c = 144.85,Å. The X-ray diffraction data were processed to a maximum resolution of 2.5,Å. The Matthews coefficient suggests the presence of two (VM = 4.01,Å3,Da,1) to four (VM = 2.0,Å3,Da,1) molecules in the asymmetric unit. Calculation of the self-rotation function shows a crystallographic fourfold symmetry axis along the z axis (, = 90°) and also a twofold symmetry axis around the z axis (, = 180°). [source] Expression, purification, crystallization and preliminary X-ray analysis of Rv3117, a probable thiosulfate sulfurtransferase (CysA3) from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2008Sarah J. Witholt The gene product of open reading frame Rv3117 from Mycobacterium tuberculosis (Mtb) strain H37Rv is annotated as encoding a probable rhodanese-like thiosulfate sulfurtransferase (MtbCysA3). MtbCysA3 was expressed and purified and then crystallized using the sitting-drop vapour-diffusion method. X-ray diffraction data were collected and processed to a maximum resolution of 2.5,Å. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 38.86, b = 91.43, c = 83.57,Å, , = 96.6°. Preliminary diffraction data shows that two molecules are present in the asymmetric unit; this corresponds to a VM of 2.4,Å3,Da,1. [source] Crystallization and preliminary crystallographic analysis of the second GAF domain of DevS from Mycobacterium smegmatisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2008Ha Yeon Cho Mycobacterium tuberculosis is known to transform into the nonreplicating persistence state under the influence of hypoxia or nitric oxide. DevS-DevR is a two-component regulatory system that mediates the genetic response for the transformation. DevS is a histidine kinase that contains two GAF domains for sensing hypoxia or nitric oxide. The second GAF from M. smegmatis DevS was crystallized using the sitting-drop vapour-diffusion method in the presence of sodium citrate and 2-propanol as precipitants. X-ray diffraction data were collected from crystals containing selenomethionine to a maximum resolution of 2.0,Å on a synchrotron beamline. The crystals belong to the hexagonal space group P61. The asymmetric unit contains one molecule, corresponding to a packing density of 2.5,Å3,Da,1. The selenium substructure was determined by the single anomalous dispersion method and structure refinement is in progress. [source] Recombinant bovine uteroglobin at 1.6,Å resolution: a preliminary X-ray crystallographic analysisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2005Victoria Von Der Decken Uteroglobin (UG) is a conserved protein which is induced by progesterone and secreted by the epithelia of various mammalian reproductive and respiratory organs. Recombinant bovine uteroglobin (recbUG), consisting of 80 amino acids with a C-terminal His6 tag, was overexpressed in Escherichia coli and purified. The protein was crystallized in two geometric forms, rhomboid and cuneate (wedge-shaped), by the hanging-drop vapour-diffusion method at 295,K. The rhomboid crystals diffracted to a maximum resolution of 1.6,Å using synchrotron radiation. These crystals belong to space group P21212, with unit-cell parameters a = 81.42, b = 82.82, c = 45.26,Å, and contain four monomers per asymmetric unit. The cuneate crystals diffracted to 2.35,Å resolution using a rotating-anode generator. These crystals belong to space group C2221, with unit-cell parameters a = 43.39, b = 93.94, c = 77.30,Å, and contain two molecules per asymmetric unit. [source] Crystallization and preliminary structural characterization of the two actin-depolymerization factors of the malaria parasiteACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Jani Huttu The malaria parasite Plasmodium depends on its actin-based motor system for motility and host-cell invasion. Actin-depolymerization factors are important regulatory proteins that affect the rate of actin turnover. Plasmodium has two actin-depolymerization factors which seem to have different functions and display low sequence homology to the higher eukaryotic family members. Plasmodium actin-depolymerization factors 1 and 2 have been crystallized. The crystals diffracted X-rays to maximum resolutions of 2.0 and 2.1,Å and belonged to space groups P3121 or P3221, with unit-cell parameters a = b = 68.8, c = 76.0,Å, and P21212, with unit-cell parameters a = 111.6, b = 57.9, c = 40.5,Å, respectively, indicating the presence of one or two molecules per asymmetric unit in both cases. [source] Two-step counterdiffusion protocol for the crystallization of haemoglobin II from Lucina pectinata in the pH range 4,9ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Carlos A. Nieves-Marrero Lucina pectinata haemoglobin II (HbII) transports oxygen in the presence of H2S to the symbiotic system in this bivalve mollusc. The composition of the haem pocket at the distal site includes TyrB10 and GlnE7, which are very common in other haem proteins. Obtaining crystals of oxyHbII at various pH values is required in order to elucidate the changes in the conformations of TyrB10 and GlnE7 and structural scenarios induced by changes in pH. Here, the growth of crystals of oxyHbII using the capillary counterdiffusion (CCD) technique at various pH values using a two-step protocol is reported. In the first step, a mini-screen was used to validate sodium formate as the best precipitating reagent for the growth of oxyHbII crystals. The second step, a pH screen typically used for optimization, was used to produce crystals in the pH range 4,9. Very well faceted prismatic ruby-red crystals were obtained at all pH values. X-ray data sets were acquired using synchrotron radiation of wavelength 0.886,Å (for the crystals obtained at pH 5) and 0.908,Å (for those obtained at pH 4, 8 and 9) to maximum resolutions of 3.30, 1.95, 1.85 and 2.00,Å for the crystals obtained at pH 4, 5, 8 and 9, respectively. All of the crystals were isomorphous and belonged to space group P42212. [source] | |||||||||||||