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  • 1
    Electronic Resource
    Electronic Resource
    Production and crystallization of virus-like particles assembled in a heterologous protein expression system (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 351-354 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It is of considerable interest to separate the processes of viral infectivity and virion assembly. Until recently this has only been possible with viruses that could be disassembled and reassembled in vitro. Even in these cases it was difficult to establish the authenticity of reassembled capsid protein because of possible irreversible damage that may have occurred to the protein during disassembly. An ideal method for the study of virus assembly is a protein expression system in which conditions are appropriate for spontaneous particle formation from freshly synthesized polypeptides. The baculovirus expression system has proven to be an excellent means to this end. Recently, this approach has been used to study the T = 3 Flock House insect virus and it has been demonstrated that subunits with the wild-type protein sequence, and with site-specific mutations that prevent particle maturation, will assemble and crystallize. This same approach has now been used at Purdue to study the T = 4 Nudaurelia ω capensis insect virus. There is no cell culture system currently available for the study of NωV, thus the expression system provides the first opportunity to study assembly under controlled conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499400123X
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  • 2
    Electronic Resource
    Electronic Resource
    A monoclinic crystal with R32 pseudo-symmetry: a preliminary report of Nodamura virus structure determination (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 580-587 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: We have crystallized Nodamura virus, a T = 3 icosahedral virus that can infect both mammalian and insect hosts. Crystals are monoclinic, with two crystallographically independent virus molecules per asymmetric unit. Packing analysis reveals a pseudo-rhombohedral (pseudo-C2 in the monoclinic setting) arrangement of virus particles in the crystal lattice. Crystals differ from the R32 symmetry by rotational and translational deviations. The rhombohedral packing arrangement and its failure to describe the exact virus packing is analyzed in detail. The icosahedral threefold axis is rotated from the body diagonal of the pseudo-rhombohedral cell, breaking the rhombohedral symmetry. The C2 pseudo-symmetry breaks down rotationally and/or translationally.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993007498
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  • 3
    Electronic Resource
    Electronic Resource
    Structure determination of coxsackievirus B3 to 3.5 Å resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 871-887 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of coxsackievirus B3 (CVB3) has been determined to 3.5 Å resolution. The icosahedral CVB3 particles crystallize in the monoclinic space group, P21, (a = 574.6, b = 302.1, c = 521.6 Å, β = 107.7°) with two virions in the asymmetric unit giving 120-fold non-crystallographic redundancy. The crystals diffracted to 2.7 Å resolution and the X-ray data set was 55% complete to 3.0,4, resolution. Systematically weak reflections and the self-rotation function established pseudo R32 symmetry with each particle sitting on a 32 special position. This constrained the orientation and position of each particle in the monoclinic cell to near face-centered positions and allowed for a total of six possible monoclinic space-group settings. Correct interpretation of the high-resolution (3.0–3.2 Å) self-rotation function was instrumental in determining the deviations from R32 orientations of the virus particles in the unit cell. Accurate particle orientations permitted the correct assignment of the crystal space-group setting amongst the six ambiguous possibilities and for the correct determination of particle positions. Real-space electron-density averaging and phase refinement, using human rhinovius 14 (HRV14) as an initial phasing model, have been carried out to 3.5 Å resolution. The initial structural model has been built and refined to 3.5 Å resolution using X-PLOR.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995002253
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  • 4
    Electronic Resource
    Electronic Resource
    Resolution of Space-Group Ambiguity and Structure Determination of Nodamura Virus to 3.3 Å resolution from Pseudo-R32 (Monoclinic) Crystals (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 738-746 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Monoclinic crystals of nodamura virus (NOV) have two virus molecules per asymmetric unit. Packing analysis reveals a pseudo-rhombohedral (pseudo-C2 monoclinic) arrangement of particles in the actual P21 space group (a = 562.1, b = 354.1, c = 612.8 Å, β = 110.9°). The R32 symmetry is broken rotationally and translationally. The pseudo-symmetry of the unit cell results in three possible monoclinic origins and also restrains the four particles in the unit cell to similar orientations. NOV particles deviate by less than 3° from the ideal orientations, causing overlap of peaks in the rotation function and the generation of peaks that were not interpretable as particle symmetry elements. The space-group ambiguity was resolved by analysing the relationship between the particle orientations determined by high-resolution rotation functions and the attenuation of peak heights in native Patterson maps. Particles were centered less than 1 Å from the R32 special positions. Three different approaches were required to identify the correct particle center. Following the solutions of the rotation and translation problems, phases were computed using the coordinates of flock house virus (FHV), another member of this virus family. The phases were improved by real-space molecular averaging with a 120-fold non-crystallographic symmetry and by solvent flattening with a spherical mask. The final model for the NOV structure was built using the 3.3 Å averaged map. While the overall subunit structure was very similar to that of other nodaviruses, FHV and black beetle virus, NOV showed distinct structural features near particle threefold and quasi-threefold axes and at the protein–RNA interfaces that are consistent with phenotype differences among the related viruses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997007427
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  • 5
    Electronic Resource
    Electronic Resource
    The structure determination of a common cold virus, human rhinovirus 14 (1987)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 43 (1987), S. 346-361 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The methods used to solve the structure of human rhinovirus 14 at 3.0 Å resolution are described in detail. The crystals are cubic, space group P213, a = 445.1 Å with 20-fold non-crystallographic redundancy and with approximately 55% solvent and RNA content. The data used to solve the structure were collected at the Cornell High Energy Synchrotron Source (CHESS) using oscillation photography. Most of the computations were performed on Purdue University's Cyber 205 supercomputer. Two heavy-atom derivative data sets from crystals soaked in 1 and 5 mM KAu(CN)2 were used to provide isomorphous phasing to 4 Å resolution, although it was subsequently shown that phases beyond 5 Å resolution were random. The phases were refined at 5 Å resolution by five cycles of real-space molecular replacement. Phase extension from 5 to 3 Å was then performed using 60 cycles of real-space molecular replacement while extending the resolution in steps of three reciprocal-lattice points at a time once every three cycles. The 3.5 Å skew-averaged map was easily interpreted and showed 811 of the 855 amino acids in the four distinct viral polypeptide chains. A complete atomic model has been built using FRODO on an Evans & Sutherland PS300 graphics system with respect to the 3.08 Å resolution electron density map. The roles of the non-crystallographic symmetry, solvent content, errors in amplitudes, orientation and translation in the molecular replacement process are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767387099306
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  • 6
    Electronic Resource
    Electronic Resource
    Increased resolution data from a large unit cell crystal collected at a third-generation synchrotron X-ray source (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 890-893 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A third-generation synchrotron source was used to collect data from crystals with a very large unit cell. There was an increase in the effective resolution of the data from 5 to 3.5 Å. Data were collected on crystals of HK97 mature empty capsids, space group P21, with unit-cell parameters a = 580, b = 625, c = 790 Å, β = 90.0°. Like other crystals with very large unit-cell dimensions, the intensity falls off rapidly as a function of resolution, with a precipitous drop beginning at 9 Å resolution. Synchrotron data from these crystals were previously observed at the CHESS F1 beamline to about 3.5 Å resolution, but the intensities could not be accurately measured beyond 5 Å. In experiments conducted at the Advanced Photon Source (APS) beamline 14-BM-C, data from identical crystals could be processed to a resolution of 3.5 Å. The lifetime of the crystals in the beam was increased from one exposure per crystal volume to between four and eight exposures per crystal volume. More than 500 images were collected in two trips, allowing the extension of the resolution of the data set and the structure determination to 3.5 Å resolution. Factors in the increased resolution may include X-ray flux, beamline geometry and low background scatter. These results suggest that other crystals with large unit cells and pronounced intensity falloff with resolution may benefit from the use of this or similar beamlines.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900005941
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  • 7
    Electronic Resource
    Electronic Resource
    A method for preventing crystal slippage in macromolecular crystallography (1977)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 10 (1977), S. 365-365 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889877013703
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  • 8
    Electronic Resource
    Electronic Resource
    Macromolecular crystallography with synchrotron radiation: collection and processing of data from crystals with a very large unit cell (1984)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 17 (1984), S. 147-153 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Hexagonal crystals of cowpea mosaic virus in space group P6122 (or its enantiomorph) with a = 451 and c = 1038 Å have been analyzed using the synchrotron X-ray source at LURE. Data were collected using an X-ray beam of size 0.18 × 0.22 mm permitting resolution of reflections along the c* direction. The beam was defined using a multiple slit system at both the monochromator and at the collimator. A helium path was used to reduce air scatter as a specimen-to-film distance of 175 mm was employed. Data to 4.3 Å resolution were recorded on each film. The films were processed to 6 Å resolution using the oscillation photograph processing package developed by Rossmann [J. Appl. Cryst. (1979), 12, 225–238] with minor modifications to the normal procedures. One film was processed to 4.3 Å resolution establishing the feasibility of intermediate resolution analysis. Statistical analysis of the processed data showed excellent correlation between symmetry-equivalent reflections. Post refinement of oscillation angles and lattice constants was very stable and led to significantly improved scaling of partially recorded reflections.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889884011213
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  • 9
    Electronic Resource
    Electronic Resource
    (E)-O-Methyl-p-nitrobenzohydroximoyl cyanide (1986)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 42 (1986), S. 1656-1657 
    Details
    ISSN: 1600-5759
    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/S0108270186091084
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  • 10
    Electronic Resource
    Electronic Resource
    2,2'-Azinodi-2-ethanenitrile (1986)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 42 (1986), S. 1657-1658 
    Details
    ISSN: 1600-5759
    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/S0108270186091072
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