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Acta Crystallographica Section A: Foundations of Crystallography (1)
Acta Crystallographica Section F: Structural Biology and Crystallization Communications (1)
Taka, Junichiro (2)
Go, Nobuhiro (1)
Jeyakanthan, Jeyaraman (1)
Kikuchi, Akihiro (1)
Kono, Hidetoshi (1)
Kuroishi, Chizu (1)
Shiro, Yoshitugu (1)
Tokuhisa, Atsushi (1)
Yutani, Katsuhide (1)
Year of Publication
Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise
Acta Crystallographica Section A: Foundations of Crystallography
A new algorithm is developed for reconstructing the high-resolution three-dimensional diffraction intensity function of a globular biological macromolecule from many quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The structural resolution is expressed as a function of the incident X-ray intensity and quantities characterizing the target molecule.
A new two-step algorithm is developed for reconstructing the three-dimensional diffraction intensity of a globular biological macromolecule from many experimentally measured quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The first step is classification of the two-dimensional patterns into groups according to the similarity of direction of the incident X-rays with respect to the molecule and an averaging within each group to reduce the noise. The second step is detection of common intersecting circles between the signal-enhanced two-dimensional patterns to identify their mutual location in the three-dimensional wavenumber space. The newly developed algorithm enables one to detect a signal for classification in noisy experimental photon-count data with as low as ∼0.1 photons per effective pixel. The wavenumber of such a limiting pixel determines the attainable structural resolution. From this fact, the resolution limit due to the quantum noise attainable by this new method of analysis as well as two important experimental parameters, the number of two-dimensional patterns to be measured (the load for the detector) and the number of pairs of two-dimensional patterns to be analysed (the load for the computer), are derived as a function of the incident X-ray intensity and quantities characterizing the target molecule.
biological macromolecules; classification of two-dimensional diffraction patterns; common intersecting circles; attainable structural resolution
Purification, crystallization and preliminary X-ray crystallographic study of the l-fuculose-1-phosphate aldolase (FucA) from Thermus thermophilus HB8
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
The crystallization and preliminary X-ray diffraction analysis of the l-fuculose-1-phosphate aldolase (FucA) from T. thermophilus HB8. Native diffraction data set was collected to a resolution of 1.9 Å.
Fuculose phosphate aldolase catalyzes the reversible cleavage of l-fuculose-1-phosphate to dihydroxyacetone phosphate and l-lactaldehyde. The protein from Thermus thermophilus HB8 is a biological tetramer with a subunit molecular weight of 21 591 Da. Purified FucA has been crystallized using sitting-drop vapour-diffusion and microbatch techniques at 293 K. The crystals belong to space group P4, with unit-cell parameters a = b = 100.94, c = 45.87 Å. The presence of a dimer of the enzyme in the asymmetric unit was estimated to give a Matthews coefficient (V M) of 2.7 Å3 Da−1 and a solvent content of 54.2%(v/v). Three-wavelength diffraction MAD data were collected to 2.3 Å from zinc-containing crystals. Native diffraction data to 1.9 Å resolution have been collected using synchrotron radiation at SPring-8.
fuculose phosphate aldolase; class II aldolases; Thermus thermophilus HB8
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