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  • 1
    Language: English
    In: Journal of Applied Crystallography, April, 2013, Vol.46, p.525(12)
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1107/S0021889813003348/abstract Byline: R. W. Alkire(1), F. J. Rotella(1), N. E. C. Duke(1) Keywords: protein crystallography; sample mounting loops; cold-streams; loop motion The purpose of this study was to determine the relative stiffness of the more common sample mounting loops used in protein crystallography experiments and to see if they were moving under the influence of the nitrogen cold-stream gas. The `stress test' involved mounting a silicon single crystal onto a loop and seeing how reproducibly a single reflection could be measured at low temperature using a photodiode detector. Once a general ranking of loop stiffness was obtained, crystals of tetragonal lysozyme were mounted in these loops to investigate if data quality was being degraded as a result of cold-stream gas-induced loop motion. Sample motion was assessed using a differential measurement based on data sets taken at two different I* orientations on the same sample. Four of the eight sample mounting loops tested showed evidence of motion in at least one lysozyme data set using typical sample sizes and normal data collection conditions. These results suggest that loop thickness is key to increased stiffness, and factors such as loop design and frozen solvent can also play an important role. Author Affiliation: (1)Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA Correspondence: (*) R. W. Alkire, e-mail: alkire@anl.gov Received 9 November 2012, accepted 1 February 2013 Supporting information: Additional Supporting Information may be found in the online version of this article Supplementary photographs. DOI:
    Keywords: Nitrogen (Chemical element) ; Lysozyme
    ISSN: 0021-8898
    Source: Cengage Learning, Inc.
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  • 2
    In: Journal of Applied Crystallography, 01 April 2013, Vol.46(2), pp.525-536
    Description: The purpose of this study was to determine the relative stiffness of the more common sample mounting loops used in protein crystallography experiments and to see if they were moving under the influence of the nitrogen cold‐stream gas. The `stress test' involved mounting a silicon single crystal onto a loop and seeing how reproducibly a single reflection could be measured at low temperature using a photodiode detector. Once a general ranking of loop stiffness was obtained, crystals of tetragonal lysozyme were mounted in these loops to investigate if data quality was being degraded as a result of cold‐stream gas‐induced loop motion. Sample motion was assessed using a differential measurement based on data sets taken at two different κ orientations on the same sample. Four of the eight sample mounting loops tested showed evidence of motion in at least one lysozyme data set using typical sample sizes and normal data collection conditions. These results suggest that loop thickness is key to increased stiffness, and factors such as loop design and frozen solvent can also play an important role.
    Keywords: Protein Crystallography ; Sample Mounting Loops ; Cold‐Streams ; Loop Motion
    ISSN: 0021-8898
    E-ISSN: 1600-5767
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  • 3
    In: Journal of Applied Crystallography, 01 April 2016, Vol.49(2), pp.415-425
    Description: At the Structural Biology Center beamline 19BM, located at the Advanced Photon Source, the operational characteristics of the equipment are routinely checked to ensure they are in proper working order. After performing a partial flat‐field calibration for the ADSC Quantum 210r CCD detector, it was confirmed that the detector operates within specifications. However, as a secondary check it was decided to scan a single reflection across one‐half of a detector module to validate the accuracy of the calibration. The intensities from this single reflection varied by more than 30% from the module center to the corner of the module. Redistribution of light within bent fibers of the fiber‐optic taper was identified to be a source of this variation. The degree to which the diffraction intensities are corrected to account for characteristics of the fiber‐optic tapers depends primarily upon the experimental strategy of data collection, approximations made by the data processing software during scaling, and crystal symmetry. A check of the flat‐field calibration of a CCD detector showed good agreement with the manufacturer's calibration. A position‐specific effect was detected that requires an additional correction to scale diffraction data properly. The source of this effect is uncorrectable using the flat‐field correction, leading to a modulation of sharp features.
    Keywords: Ccd Detectors ; Fiber‐Optic Tapers ; Flat‐Field Calibration ; Data Scaling ; Anomalous Signal
    ISSN: 1600-5767
    ISSN: 00218898
    E-ISSN: 1600-5767
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  • 4
    Language: English
    In: Journal of the American Chemical Society, 09/1981, Vol.103(19), pp.5885-5890
    ISSN: 0002-7863
    E-ISSN: 15205126
    Source: American Chemical Society (via CrossRef)
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  • 5
    Language: English
    In: Z. Kristallogr, 01 January 2002, Vol.217(7-8 ; 2002)
    Description: Journal Article.
    Keywords: Materials Science ; Crystallography ; Materials ; Anl ; Engineering ; Geology
    ISSN: 0044-2968
    E-ISSN: 2366-1798
    E-ISSN: 21967105
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  • 6
    Language: English
    In: Journal of Applied Physics, October 1982, Vol.53(10), pp.6751-6756
    Description: The crystal structure of α‐SiO 2 (low quartz) has been refined at 296, 78, and 13 K from time‐of‐flight neutron powder diffraction data. The major effect of temperature from 296 to 78 K is a nearly rigid body rotation of the SiO 4 tetrahedra. Below 78 K, tetrahedral rotation is substantially reduced giving rise to a much smaller thermal expansion. A comparison of the volume dependence of the Si‐O‐Si angle, the rotation angle for SiO 4 tetrahedra and the c / a ratio suggests that the mechanism for expansion may be changing from tetrahedral rotation to tetrahedral distortion at the lowest temperatures. The inverse linear relation between the mean Si‐O bond distance and −sec(Si‐O‐Si) which has been observed for silica minerals at both ambient and high‐temperature conditions appears to be consistent with the structural variations that occur at low temperatures.
    Keywords: Materials Science ; Quartz ; Crystal Structure ; Thermal Expansion ; Bond Angle ; Bond Lengths ; Experimental Data ; Lattice Parameters ; Low Temperature ; Mathematical Models ; Medium Temperature ; Neutron Diffraction ; Powders ; Space Dependence ; Temperature Effects ; Tetragonal Lattices ; Time-Of-Flight Method ; Ultralow Temperature ; Very Low Temperature ; Chalcogenides ; Coherent Scattering ; Crystal Lattices ; Data ; Diffraction ; Dimensions ; Expansion ; Information ; Length ; Minerals ; Numerical Data ; Oxide Minerals ; Oxides ; Oxygen Compounds ; Scattering ; Silicon Compounds ; Silicon Oxides ; 360603 - Materials- Properties;
    ISSN: 0021-8979
    E-ISSN: 1089-7550
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  • 7
    Language: English
    In: The Journal of Chemical Physics, 01 November 1983, Vol.79(9), pp.4522-4531
    Description: The structures of the single‐phase, well‐crystallized family of hydrides Zr 3 V 3 OD x for x =0, 1.86, 2.85, and 4.93 have been refined by the Rietveld method from neutron powder diffraction data taken at 298 K. The alloy and the three deuterides studied all possess the η‐carbide structure (cubic F d 3 m ; origin at 4̄3 m ). Deuterium is found to occupy four different tetrahedral interstices preferentially. Sites with the largest number of Zr near neighbors appear to fill first unless occupation is hindered by nearby oxygen or simultaneously occupied deuterium sites. The volume expansion per number of deuterium atoms is nearly linear, even though the lowest stable hydride concentration at 298 K is near Zr 3 V 3 OD 1.5 and markedly nonlinear distortions occur within the unit cell as different sites fill.
    Keywords: Legierung ; Chemische Zusammensetzung ; Kristallstruktur ; Gitterplatz ; Neutronenbeugung ; Experimentelle Untersuchung ; Konzentrationseinfluss ; Isotopeneffekt ; Chemistry ; Physics;
    ISSN: 0021-9606
    E-ISSN: 1089-7690
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  • 8
    Language: English
    In: Biochemistry, 01 January 1999, Vol.38(15 ; 1999)
    Description: IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K{sub m} for NAD (1180 {mu}M) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 {angstrom} with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione {beta}-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.
    Keywords: Materials Science ; Particle Accelerators ; Advanced Photon Source ; Antimicrobial Agents ; Biology ; Catalysis ; Crystal Structure ; Data ; Dimers ; Enzymes ; Evaluation ; Kinetics ; Mutants ; Nad ; Oxidoreductases ; Proteins ; Sensitivity ; Streptococcus ; Substrates ; Synchrotron Radiation ; Synthesis ; Wiggler Magnets ; Biology ; Chemistry ; Anatomy & Physiology
    ISSN: 0006-2960
    E-ISSN: 1520-4995
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  • 9
    Language: English
    In: Inorganic Chemistry, 09/1986, Vol.25(20), pp.3590-3593
    Description: The structure of the low-temperature phase of Mg/sub 2/NiD/sub 4/ was determined from time-of-flight neutron powder diffraction data collected at 298 K. It has monoclinic symmetry (space group C2/c, a = 14.343 (5) A, b = 6.4038 (10) A, c = 6.4830 (13) A, ..beta.. = 113.52 ()/sup 0/, Z = 8) and contains four symmetry-independent D atoms. As expected, the D atoms surround the Ni atoms in a nearly regular tetrahedral configuration (average bond lengths Ni-D = 1.54 A, average bond angles D-Ni-D = 109.4/sup 0/). Microtwinning parallel to (011) leads to severe anisotropic broadening of the diffraction peaks.
    Keywords: 08 Hydrogen ; Deuterium Compounds ; Crystal Structure ; Magnesium Compounds ; Nickel Compounds ; Bond Angle ; Bond Lengths ; Experimental Data ; Medium Temperature ; Monoclinic Lattices ; Neutron Diffraction ; Powders ; Space Groups ; Time-Of-Flight Method ; Alkaline Earth Metal Compounds ; Coherent Scattering ; Crystal Lattices ; Data ; Diffraction ; Dimensions ; Hydrogen Compounds ; Information ; Length ; Numerical Data ; Scattering ; Transition Element Compounds ; 080201 - Hydrogen- Chemisorption Storage;
    ISSN: 0020-1669
    E-ISSN: 1520-510X
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  • 10
    Language: English
    In: The Journal of Chemical Physics, 01 December 1994, Vol.101(11), pp.9333-9337
    Description: We have used neutron diffraction on polycrystalline samples of AnF 4 (An=Th, U, and Np) to examine the structures. All are isostructural with monoclinic space group C 2/ c . The structure of UF 4 has been examined in some detail as a function of temperature. The volume of the unit cell has a minimum not at lowest temperature (15 K) examined, but rather at ∼350 K. ThF 4 also has a larger volume at low rather than room temperature; suggesting that this effect is caused by structural rather than electronic (as ThF 4 has no 5 f electrons) interactions. An examination of the coordination around the two independent An sites in UF 4 shows that the fluorine configuration changes appreciably around An2 as a function of temperature. At low temperatures the distorted cubic antiprism structure is considerably more ‘‘puckered’’ than at higher temperatures. This puckering requires more volume for the molecule, thus causing the volume to expand as the temperature is lowered. The temperature factors and the interatomic distances vary smoothly with temperature and show no unusual behavior.
    Keywords: Materials Scienceneptunium Fluorides ; Lattice Parameters ; Thorium Fluorides ; Uranium Fluorides ; Actinide Compounds ; Interatomic Distances ; Monoclinic Lattices ; Neutron Diffraction ; Polycrystals ; Temperature Dependence ; Temperature Range 0013-0065 K ; Temperature Range 0065-0273 K ; Temperature Range 0273-0400 K ; Volume ; Coherent Scattering ; Crystal Lattices ; Crystal Structure ; Crystals ; Diffraction ; Distance ; Fluorides ; Fluorine Compounds ; Halides ; Halogen Compounds ; Neptunium Compounds ; Scattering ; Temperature Range ; Thorium Compounds ; Transuranium Compounds ; Uranium Compounds;
    ISSN: 0021-9606
    E-ISSN: 1089-7690
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