Structural variability and the incoherent addition of scattered intensities in single-particle diffraction.
X-ray lasers may allow structural studies on single particles and biomolecules without crystalline periodicity in the samples. We examine here the effect of sample dynamics as a source of structural heterogeneity on the resolution of the reconstructed image of a small protein molecule. Structures from molecular-dynamics simulations of lysozyme were sampled and aligned. These structures were then used to calculate diffraction patterns corresponding to different dynamic states. The patterns were incoherently summed and the resulting data set was phased using the oversampling method. Reconstructed images of hydrated and dehydrated lysozyme gave resolutions of 3.7 A and 7.6 A , respectively. These are significantly worse than the root-mean-square deviation of the hydrated ( 2.7 A for all atoms and 1.45 A for C-alpha positions) or dehydrated ( 3.7 A for all atoms and 2.5 A for C-alpha positions) structures. The noise introduced by structural dynamics and incoherent addition of dissimilar structures restricts the maximum resolution to be expected from direct image reconstruction of dynamic systems. A way of potentially reducing this effect is by grouping dynamic structures into distinct structural substates and solving them separately.
Maia
Filipe R N C
FR
Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, Uppsala SE-75124, Sweden. filipe@xray.bmc.uu.se
Ekeberg
Tomas
T
Tîmneanu
Nicuşor
N
van der Spoel
David
D
Hajdu
Janos
J
D007091:Image Processing, Computer-Assisted; D056004:Molecular Dynamics Simulation; D009068:Movement; D009113:Muramidase / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D014732:Vibration; D014961:X-Ray Diffraction
D011506:Proteins; D009113:Muramidase