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  • American Physical Society (APS)
  • International Union of Crystallography (IUCr)
  • 1990-1994  (7,163)
Collection
Publisher
Years
Year
  • 1
    Electronic Resource
    Electronic Resource
    Molecular scene analysis: the integration of direct-methods and artificial-intelligence strategies for solving protein crystal structure (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 168-178 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A knowledge-based approach to crystal structure determination is presented. The approach integrates direct-methods and artificial-intelligence strategies to rephrase the structure determination process as an exercise in scene analysis. A general joint probability distribution framework, which allows the incorporation of isomorphous replacement, anomalous scattering and a priori structural information, forms the basis of the direct-methods strategies. The accumulated knowledge on crystal and molecular structures is exploited through the use of artificial-intelligence strategies, which include techniques of knowledge representation, search and machine learning.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499200917X
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  • 2
    Electronic Resource
    Electronic Resource
    Executive Secretary (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 427-427 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993099731
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  • 3
    Electronic Resource
    Electronic Resource
    Nucleic acid targeted drug design edited by C. L. Propst and T. Perun (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 428-428 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499309972X
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  • 4
    Electronic Resource
    Electronic Resource
    Crystallization of the OP-G2 Fab fragment: a fibrinogen mimic with specificity for the platelet glycoprotein IIb/IIIa (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 421-422 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The OP-G2 monoclonal antibody binds to the platelet integrin, gpIIb/IIIa, in a mode that mimics fibrinogen binding. The specificity of this antibody is mediated by the third complementarity-determining region (CDR3) loop of the immunoglobulin heavy chain which contains a sequence (RYD) related to the RGD recognition sequence of fibrinogen. The OP-G2 Fab fragment has been crystallized by vapor diffusion from solutions containing polyethylene glycol and imidazole malate (pH 5.6). The crystals belong to space group P21212 with a = 93.1, b = 83.8 and c = 53.7 Å. One Fab molecule is present in the asymmetric unit. A complete data set to 2.0 Å resolution has been collected.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993002501
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  • 5
    Electronic Resource
    Electronic Resource
    International tables for crystallography. Vol. C. Mathematical, physical and chemical tables edited by A. J. C. Wilson (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 428-428 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993099718
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  • 6
    Electronic Resource
    Electronic Resource
    Entropy phase dynamics (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 75-85 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The entropy-dynamics method seeks maxima for the entropy of the electron density for N atoms in a crystal cell, when the Fourier amplitudes are fixed, but their phases are unknown. By analogy with molecular dynamics, the effective potential energy is the negative entropy V = −NS. The kinetic energy is proportional to the squared velocities of the electron densities at grid points in the map. It reduces to a sum of Fourier-mode rotor energies. Each rotor angle experiences a couple equal to the phase gradient of S, and local dynamical equilibrium yields a Boltzmann distribution of S. Discrete phase angles (e.g. signs) are treated as quantized rotor modes. The distributions depend on a popularity function of the entropy histogram. Trial calculations have been made of phase averages and correlations in a centrosymmetric projection of the membrane protein bacteriorhodopsin. The maximum-entropy solution and the correct solution do not always coincide.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992008102
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  • 7
    Electronic Resource
    Electronic Resource
    Structure determination of aldose reductase: joys and traps of local symmetry averaging (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 246-256 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of aldose reductase, a monomeric enzyme of 314 amino acids which crystallizes in space group P1 with four monomers per asymmetric unit, has been solved using a combination of single isomorphous replacement (SIR), solvent flattening and local symmetry averaging. The self rotation showed evidence of 222 local symmetry. The map calculated from the original single isomorphous replacement phases showed a clear solvent envelope but was uninterpretable. A first averaging attempt failed because the molecular envelope obtained from the SIR map weighted with monomer correlation was too small and the averaging was biased by low-resolution truncation. A second attempt with an enlarged envelope and including low-resolution reflections succeeded in refining phases at 3.5 Å resolution but failed to extend them correctly. Rigid-body refinement of a partial model based on the 3.5 Å map calculated from refined phases showed significant departures from the 222 symmetry. A third averaging attempt using the improved symmetry succeeded in producing a clear map with phases extended to 3.07 Å resolution. This map revealed a (β/α)8 fold, not previously found in NADPH-dependent enzymes. This work shows the importance of mask definition and local symmetry elements accuracy for averaging, and describes a method for improving these parameters.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499200773X
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  • 8
    Electronic Resource
    Electronic Resource
    Structure at pH 6.5 of ferredoxin I from Azotobacter vinelandii at 2.3 Å resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 272-281 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Ferredoxin I from Azotobacter vinelandii (AvFdI) is an iron–sulfur protein composed of 106 amino acids, seven Fe atoms and eight inorganic S* atoms. A crystallographic redetermination of its structure showed the originally reported structure to be incorrect. We report here the crystal structure of AvFdI at pH 6.5. Extensive refinement has led to a final R value of 0.170 for all 6986 non-extinct reflections in the range 10–2.3 Å using a solvent model which includes 98 discrete solvent atoms with occupancies between 0.3 and 1.0 and an average B value of 22.5 Å2. The first half of the peptide chain closely resembles that of the 55-residue ferredoxin from Peptococcus aerogenes (PaFd), while the remainder consists of three turns of helix and a series of loops which form a cap over part of the molecular core. Despite the similarities in structure and surroundings, the corresponding 4Fe4S* clusters in PaFd and AvFdI have strikingly different redox potentials; a possible explanation has been sought in the differing hydration models for the two molecules.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992007248
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  • 9
    Electronic Resource
    Electronic Resource
    The mechanism of iron uptake by transferrins: the structure of an 18 kDa NII-domain fragment from duck ovotransferrin at 2.3 Å resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 292-304 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular structure of an iron-containing 18 kDa fragment of duck ovotransferrin, obtained by proteolysis of the intact protein, has been elucidated by protein crystallographic techniques at 2.3 Å resolution. This structure supports a mechanism of iron uptake in the intact protein whereby the binding of the synergistic (bi)carbonate anion is followed by binding of the metal with the lobe in the open configuration. These stages are then followed by domain closure in which the aspartic acid residue plays a further key role, by forming an interdomain hydrogen-bond interaction in addition to serving as a ligand to the iron. This essential dual role is highlighted by model building studies on the C-terminal lobe of a known human variant. In this variant a mutation of a glycine by an arginine residue enables the aspartic acid to form an ion pair and reduce its effectiveness for both metal binding and domain closure. The X-ray structure of the 18 kDa fragment strongly suggests that the histidine residue present at the iron binding site of the intact protein and arising from the second interdomain connecting strand has been removed during the preparative proteolysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992012101
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  • 10
    Electronic Resource
    Electronic Resource
    The structure of an idarubicin–d(TGATCA) complex at high resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 311-317 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of the DNA hexamer d(TGATCA) complexed with the anthracycline antibiotic idarubicin has been determined at 1.6 Å resolution. The asymmetric unit consists of a single hexamer oligonucleotide strand, one drug molecule and 35 water molecules. The complex crystallizes in the tetragonal space group P41212, Z = 8 with lattice dimensions of a = b = 28.19 (3), c = 52.77 (4) Å, V = 41 935 A3. The structure is isomorphous with a series of hexamer–anthracycline complexes and was solved by molecular replacement. Restrained least-squares methods interspersed with computer-graphics map inspection and model manipulation were used to refine the structure. The R factor is 0.22 for 2032 reflections with F ≥ 3σ(F) in the resolution range 8.0–1.6 Å. The self-complementary DNA forms a distorted B-DNA double helix with two idarubicin molecules intercalated in the d(TpG) steps of the duplex. The duplex is formed by utilization of a crystallographic twofold axis of symmetry. The idarubicin chromophore is oriented at right angles to the long axis of the DNA base pairs with the anthracycline amino-sugar moiety positioned in the minor groove. Our structure determination allows for comparison with a d(CGATCG)–idarubicin complex recently reported. Despite the sequence alteration at the intercalation step, the structures are very similar. The geometry of the intercalation and the nature of the interactions are conserved irrespective of the DNA sequence involved in the binding.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992009983
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