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  • Nature Publishing Group  (15)
  • International Union of Crystallography (IUCr)  (10)
  • 1
    Electronic Resource
    Electronic Resource
    The Use of Partial Reflections for Scaling and Averaging X-ray Area-Detector Data (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 31 (1998), S. 708-717 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Frozen crystals of proteins, nucleic acids or other biological macromolecules often have mosaic spreads comparable to the maximum useful oscillation angles. It is, therefore, necessary to develop scaling methods that are independent of the exclusive use of full reflections. The Hamilton, Rollett and Sparks [Acta Cryst (1965), 18, 129–130] procedure for scaling frames of X-ray area-detector data has been generalized to utilize partial reflections by adding intensities of partial reflections from consecutive frames (method 1) or by correcting intensities of partial reflections, using a model to calculate the reflection partiality (method 2). Both methods have been applied to scaling and averaging of data-sets collected on crystals of biological macromolecules. The agreement factors of the scaled data are better when using method 1, although it often fails when there are rotation gaps between successive images or when the data redundancy is low. Method 2 is more stable and versatile, allowing scaling of data-sets with incompletely measured reflections and low redundancy. The major drawback of method 2 is its sensitivity to inaccuracy in calculated partiality. The actual values of the scale factors obtained with the two methods are within 5%. However, when the true value of the scale factor changes dramatically between consecutive frames (e.g. due to beam dumps and refills at a synchrotron source), the results of the two methods can differ by as much as 15% because method 1 produces physically wrong results. The scaling algorithm implemented in the commercially available program SCALEPACK is vulnerable to the same problems as method 1.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889898004361
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular structure of NAD (1976)
    [s.l.] : Nature Publishing Group
    Nature 262 (1976), S. 726-726 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] VIWAMITRA1 has speculated on the structure of free NAD which he then extrapolates to the NAD conformation when bound to enzymes. Unfortunately, he has neglected to take into account the extensive results which have been obtained during the past five years on the conformation of NAD when bound to ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/262726b0
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  • 3
    Electronic Resource
    Electronic Resource
    When it's better to lie low (1995)
    [s.l.] : Nature Publishing Group
    Nature 375 (1995), S. 275-276 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] IN 1981, Wiley and co-workers1 reported the atomic structure of haemagglutinin, a spike-like surface glycoprotein of influenza virus. This and subsequent work led to an explanation of the occurrence of flu pandemics2 and determination of the site of binding to the sialic acid ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/375275a0
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular replacement – historical background (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1360-1366 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A review is given of the mathematical procedures required for a molecular-replacement structure determination. These apply equally to the more frequently encountered situations where a known homologous structure can be used as a search model and to phase determination in the presence of non-crystallographic symmetry (NCS). In general, the former represents improper NCS between two different unit cells, whereas the latter occurs when there is proper NCS within one unit cell.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901009386
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  • 5
    Electronic Resource
    Electronic Resource
    A General Phasing Algorithm for Multiple MAD and MIR Data (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 159-174 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A phasing algorithm is presented for combining multiple wavelength anomalous dispersion (MAD) data from multiple types of anomalous scatterers, either in the same or in different derivative crystals, as well as for combining MAD data with multiple isomorphous replacement (MIR) data from different derivative crystals. A heavy-atom phasing and refinement program originally written by Rossmann [(1967) HATOMLSQ program, Purdue University, West Lafayette, Indiana, USA] has been modified to refine the parameters that define the anomalous and isomorphous scatterers and to determine protein phases by using all MAD and MIR derivatives simultaneously. The technique allows for appropriate weighting of every data set, including the native data, which contains neither an anomalous nor an isomorphous component. This method is a generalization of currently used heavy-atom methods. Numerical tests are presented for different experimental scenarios, including a double MAD experiment on the same crystal (diffraction data at two absorption edges), combination of two MAD experiments on different crystals, and combination of MAD data with MIR data from multiple crystals. An appendix shows how the Karle equations used in MAD phasing can be reformulated as a particular case of this algorithm.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997010469
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  • 6
    Electronic Resource
    Electronic Resource
    Data processing (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1631-1640 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: X-ray diffraction data processing proceeds through indexing, pre-refinement of camera parameters and crystal orientation, intensity integration, post-refinement and scaling. The DENZO program has set new standards for autoindexing, but no publication has appeared which describes the algorithm. In the development of the new Data Processing Suite (DPS), one of the first aims has been the development of an autoindexing procedure at least as powerful as that used by DENZO. The resultant algorithm will be described. Another major problem which has arisen in recent years is scaling and post-refinement of data from different images when there are few, if any, full reflections. This occurs when the mosaic spread approaches or exceeds the angle of oscillation, as is usually the case for frozen crystals. A procedure which is able to obtain satisfactory results for such a situation will be described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999008379
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  • 7
    Electronic Resource
    Electronic Resource
    Structure Determination of the \boldvarphiX174 Closed Procapsid (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 878-890 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of a procapsid of the single-stranded DNA bacteriophage φX174 was determined to 3.5 Å resolution. The crystal space group was I213 with a unit-cell length of 774 Å. The unit cell contained 16 icosahedral virus particles, each situated on a crystallographic three-fold axis. Thus, there are two independent one-thirds of a particle per asymmetric unit, and a total of 40-fold non-crystallographic redundancy. To aid in the interpretation of the packing arrangement, crystals were prepared for thin sectioning and analyzed by electron microscopy. Oscillation X-ray diffraction data was collected on image plates using synchrotron radiation and oscillation angles of either 0.25 or 0.30°. A low-resolution 6.5 Å data set collected from a single frozen crystal was particularly helpful in the structure determination, because of its completeness and internal consistency. The initial particle orientations were determined using self-rotation functions, while the initial position of one particle was determined from a Patterson map. The structure was solved by molecular replacement real-space averaging using a model based on a cryo-electron microscopy reconstruction as a starting point for the phase determination. The initial structure determination used the data between 20 and 13 Å resolution, which was then extended one reciprocal lattice point at a time to 6.5 Å resolution. At this point, a 3.5 Å resolution data set compiled from a number of crystals collected at 277 K was introduced. Phase extension and averaging continued to 3.5 Å resolution after re-determining the particle positions and orientations. The amino-acid sequences of most of the D, F and G proteins and part of the B protein could be unambiguously built into the 3.5 Å electron-density map. Partial crystallographic refinement yielded an R factor of 31.6%, consistent with the relatively low resolution and lack of completeness of the data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998002467
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  • 8
    Electronic Resource
    Electronic Resource
    Purification, crystallization and initial X-ray analysis of the head–tail connector of bacteriophage φ29 (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1187-1190 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The head–tail connector of bacteriophage φ29, an oligomer of gene product 10 (gp10), was crystallized into various forms. The most useful of these were an orthorhombic P22121 form (unit-cell parameters a = 143.0, b = 157.0, c = 245.2 Å), a monoclinic C2 form (a = 160.7, b = 143.6, c = 221.0 Å, β = 97.8°) and another monoclinic C2 form (a = 177.0, b = 169.1, c = 185.2 Å, β = 114.1°). Frozen crystals diffracted to about 3.2 Å resolution. There is one connector per crystallographic asymmetric unit in each case. Rotation functions show the connector to be a dodecamer. Translation functions readily determined the position of the 12-fold axis in each unit cell. The structure is being determined by 12-fold electron-density averaging within each crystal and by averaging between the various crystal forms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900009239
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  • 9
    Electronic Resource
    Electronic Resource
    Structure determination of the head–tail connector of bacteriophage φ29 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1260-1269 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The head–tail connector of bacteriophage φ29 is composed of 12 36 kDa subunits with 12-fold symmetry. It is the central component of a rotary motor that packages the genomic dsDNA into preformed proheads. This motor consists of the head–tail connector, surrounded by a φ29-encoded, 174-base, RNA and a viral ATPase protein, both of which have fivefold symmetry in three-dimensional cryo-electron microscopy reconstructions. DNA is translocated into the prohead through a 36 Å diameter pore in the center of the connector, where the DNA takes the role of a motor spindle. The helical nature of the DNA allows the rotational action of the connector to be transformed into a linear translation of the DNA. The crystal structure determination of connector crystals in space group C2 was initiated by molecular replacement, using an approximately 20 Å resolution model derived from cryo-electron microscopy. The model phases were extended to 3.5 Å resolution using 12-fold non-crystallographic symmetry averaging and solvent flattening. Although this electron density was not interpretable, the phases were adequate to locate the position of 24 mercury sites of a thimerosal heavy-atom derivative. The resultant 3.2 Å single isomorphous replacement phases were improved using density modification, producing an interpretable electron-density map. The crystallographically refined structure was used as a molecular-replacement model to solve the structures of two other crystal forms of the connector molecule. One of these was in the same space group and almost isomorphous, whereas the other was in space group P21212. The structural differences between the oligomeric connector molecules in the three crystal forms and between different monomers within each crystal show that the structure is relatively flexible, particularly in the protruding domain at the wide end of the connector. This domain probably acts as a bearing, allowing the connector to rotate within the pentagonal portal of the prohead during DNA packaging.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901010435
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  • 10
    Electronic Resource
    Electronic Resource
    Fitting atomic models into electron-microscopy maps (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1341-1349 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 Å resolution can produce structural information that is accurate to about 2.2 Å resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the former of which can be off by up to 5%. It is also necessary to determine the relative height of density by using a suitable scaling function. Difference maps can identify, for instance, sites of glycosylation, the position of which helps to fit the component structures into the EM density maps. Examples are given from the analysis of alphaviruses, rhinovirus–receptor interactions and poliovirus–receptor interactions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900009562
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