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  • 1
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 60-68 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The octapeptide octreotide crystallizes with three peptide molecules and about 20% water in the asymmetric unit, and in many ways possesses diffraction properties similar to those of a `mini-protein' consisting of 24 amino-acid residues. It diffracts to about 1.0 Å but data in the range 1.4–1.0 Å are weak. It provides a suitable test of different macromolecular X-ray data-collection techniques, especially of their ability to measure weak reflections accurately. In contrast to typical proteins it is possible to perform a full anisotropic refinement, that we believe provides a more objective test of the quality of the data than the internal consistency of equivalent reflections. We have collected a total of six data sets. The X-ray sources included synchrotron radiation, Cu Kα rotating anodes and Mo Kα sealed tubes; position-sensitive two-dimensional detectors from four manufacturers and a four-circle diffractometer with scintillation counter were employed. Two of the six data sets were collected at low temperature. Reasonable anisotropic refinement was possible with all area-detector data sets, although significant differences in the precision of the final model were observed. In addition we tested the ability of automated Patterson interpretation to solve the structure using the six independent data sets. The structure solution was only successful using the synchrotron or rotating-anode data sets, i.e. for the more intense sources. It appears that for structure solution the maximum resolution of the data is critical, whereas for refinement the accuracy of the data is more important.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 41 (1985), S. 262-268 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method is presented that attempts to exploit all the a priori available information in order to locate a fragment of known geometry in the unit cell. Whereas the orientation of the search model is determined by a conventional but highly automated real-space Patterson rotation search, its position in the cell is found by maximizing the weighted sum of the cosines of a small number of strong translation-sensitive triple-phase invariants, starting from random positions. A Patterson minimum function based on intermolecular vectors is calculated only for those solutions that do not give rise to intermolecular contacts shorter than a preset minimum. This procedure avoids the time-consuming refinement in Patterson space and should be especially efficient for large structures. Finally, the best solutions are sorted according to a figure of merit based upon the agreement with the Patterson function, the triple-phase consistency and an R index involving Eobs and Ecalc. Tests with about 30 known structures, using search fragments taken from other published structures or from force-field calculations, have indicated that this novel combination of Patterson and direct methods is reliable and widely applicable. A few selected examples demonstrate the power of the computer program PATSEE, which is compatible with SHELX84 and will be distributed together with it. PATSEE is valid and efficient for all space groups and imposes no limits on the number of atoms or data. The orientation search for a single fragment allows one additional degree of torsional freedom, and up to two fragments may be translated simultaneously.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 23 (1967), S. 35-38 
    ISSN: 0001-5520
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 18-23 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Conventional small-molecule methods of solving the phase problem from native data alone, without the use of heavy-atom derivatives, known fragment geometries or anomalous dispersion, have been tested on 0.9 Å resolution data for two small proteins: rubredoxin, from Desulfovibrio vulgaris, and crambin. The presence of three disulfide bridges in crambin and an FeS4 unit in rubredoxin enabled automated Patterson interpretation as well as direct methods to be tried. Although both structures were already well established, the known structures were not used in the phasing attempts, except for identifying successful solutions. Direct methods were not successful for crambin, although the correct phases were stable to phase refinement and gave figures of merit clearly superior to any obtained in the ca 500 000 random starting phase sets that were refined. It appears that the presence of an iron atom in rubredoxin reduces the scale of the search problem by many orders of magnitude, but at the cost of producing `over-consistent' phase sets that overemphasize the iron atom and involve partial loss of enantiomorph information. However, about 1% of direct-methods trials were successful for rubredoxin, giving mean phase errors of about 56° (for all E 〉 1.2) that could be reduced to about 20° by standard E-Fourier recycling methods. Limiting the resolution of the data degraded the quality of the solutions and suggested that the limiting resolution for routine direct-methods solution of rubredoxin is about 1.2 Å. With the 0.9 Å data, automated Patterson interpretation convincingly finds the three disulfide bridges in crambin and the FeS4 unit in rubredoxin, and in both cases E-Fourier recycling starting from these `heavier' atoms yields almost the complete structure. Whereas crambin could only be solved in this way at very high resolution, rubredoxin could be solved by Patterson interpretation down to 1.6 Å. These results emphasize the benefits of collecting protein data to the highest possible resolution, and indicate that when a few `heavier' atoms are present, it may prove possible in favorable cases to solve the phase problem from a single native data set collected to `atomic resolution'.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 48-59 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Octreotide, a synthetic somatostatin analogue, is an octapeptide with one disulfide bridge. Crystals of octreotide are orthorhombic, space group P212121, a = 18.458 (5), b = 30.009 (7), c = 39.705 (27) Å, with three molecules of octapeptide, one ordered oxalate dianion and 52 water molecules in the asymmetric unit. Complete protonation of the NH2 groups (as assumed in the refinement) would require three oxalate dianions in the asymmetric unit for charge neutrality; a chemical analysis indicated that four are present. In either case they are so disordered that they cannot be distinguished from the water molecules. The 18 951 unique reflections (Rsym = 0.026) used for structure solution and refinement were recorded with the EMBL imaging-plate scanner using synchrotron radiation. The structure was solved by Patterson interpretation, locating the three disulfide bridges, followed by tangent phase expansion and E-Fourier recycling. The anisotropic refinement against all F2 data between 1.04 and 10.0 Å resolution by blocked restrained full-matrix least-squares techniques converged to a conventional R index based on F of 0.084 [I 〉 2a(I) and 10.0 〉 d 〉 1.04 Å] and wR2, the weighted R-index on F2, of 0.246 (for all data). One peptide molecule adopts a flat β-sheet structure; the other two possess different irregular backbone conformations, but are similar to each other. All three molecules have a distorted type II′ β-turn around the D-Trp-Lys region, but exhibit different side-chain conformations. The crystal structure is stabilized by a network of inter- and intramolecular hydrogen bonds.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cytochrome c6, a plastocyanin functionally interchangeable electron carrier between the chlorophyll molecule P700 of photosystem I and cytochrome f from cytochrome b6f complex, has been isolated from the green alga Monoraphidium braunii and crystallized by the vapour-diffusion technique in sodium citrate. Crystals belong to space group R3, with cell dimensions a = b = 51.93 (5) and c = 80.5 (1) Å (hexagonal axes), with one molecule per asymmetric unit. They diffract beyond 1.9 Å under a Cu Kα rotating-anode source, with an anomalous signal that allows the positioning of the heme Fe atom in the unit cell.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 467-473 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A number of extensions to the multisolution approach to the crystallographic phase problem are discussed in which the negative quartet relations play an important role. A phase annealing method, related to the simulated annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution. The ideas presented here are incorporated in the program system SHELX-90; the philosophical and mathematical background to the direct-methods part (SHELXS) of this system is described.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 158-160 
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 1026-1028 
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
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