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. 2010 Mar 15;18(6):5713-23.
doi: 10.1364/OE.18.005713.

Femtosecond protein nanocrystallography-data analysis methods

Richard A Kirian  1 , Xiaoyu Wang, Uwe Weierstall, Kevin E Schmidt, John C H Spence, Mark Hunter, Petra Fromme, Thomas White, Henry N Chapman, James Holton
Affiliations

Femtosecond protein nanocrystallography-data analysis methods

Richard A Kirian et al. Opt Express. .

Abstract

X-ray diffraction patterns may be obtained from individual submicron protein nanocrystals using a femtosecond pulse from a free-electron X-ray laser. Many "single-shot" patterns are read out every second from a stream of nanocrystals lying in random orientations. The short pulse terminates before significant atomic (or electronic) motion commences, minimizing radiation damage. Simulated patterns for Photosystem I nanocrystals are used to develop a method for recovering structure factors from tens of thousands of snapshot patterns from nanocrystals varying in size, shape and orientation. We determine the number of shots needed for a required accuracy in structure factor measurement and resolution, and investigate the convergence of our Monte-Carlo integration method.

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Figures

Fig. 1
Fig. 1
(a). Log scaled simulation of a PS1 X-ray diffraction pattern for a 500nm crystallite at 2 keV, 1.5 mrad beam divergence, 0.1% FWHM energy spread, and background due to 1 μm3 of water. Diffraction at edges corresponds to about 0.94 nm resolution. Polarization factor and detector pixel solid angles are included, and Poisson noise is included assuming that the detector counts single photons. (b). Enlargement of Fig. 1(a), showing shape-transforms around each lattice point.
Fig. 2
Fig. 2
Crystallographic R-factor plotted against number of crystallites in random orientations merged after indexing. Colors indicate the threshold value δt. Solid lines represent simulations including Gaussian size distribution, photon noise, and water background. Dashed lines are for comparison to simulations without photon noise (*) and without noise or size distribution (**).
Fig. 3
Fig. 3
Comparison of true structure factors (o) to the Monte-Carlo integrated structure factors (x) for a threshold value of δt = 0.0047 nm−1. Size variation and noise effects are included.
Fig. 4
Fig. 4
The number of unique reflections recorded as a function of the number of crystallites. Colors indicate the threshold value δ.
See this image and copyright information in PMC

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