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Data-processing workflow for single-particle imaging experiments at X-ray free-electron lasers is presented. The analysis developed here revealed nanoscale features of the PR772 virus with a resolution better than 10 nm and without any symmetry constraints.

We show that the combination of X-ray scattering with a nanofocused beam and X-ray cross correlation analysis is an efficient means for the full structural characterization of mesocrystalline nanoparticle assemblies with a single experiment. We analyze several hundred diffraction patterns of individual sample locations, i.e. individual grains, to obtain a meaningful statistical distribution of the superlattice and atomic lattice ordering. Simultaneous small-and wide-angle X-ray scattering of the same sample location allows us to determine the structure and orientation of the superlattice as well as the angular correlation of the first two Bragg peaks of the atomic lattices, their orientation with respect to the superlattice, and the average orientational misfit due to local structural disorder. This experiment is particularly advantageous for synthetic mesocrystals made by the simultaneous self-assembly of colloidal nanocrystals and surfacefunctionalization with conductive ligands. While the structural characterization of such materials has been challenging so far, the present method now allows correlating mesocrystalline structure with optoelectronic properties. Mesocrystals (MC) are three-dimensional arrays of iso-oriented single-crystalline particles with an individual size between 1 -1000 nm. [1][2][3][4][5] Their physical properties are largely determined by structural coherence, for which the angular correlation between their individual atomic lattices and the underlying superlattice of nanocrystals (NC) is a key ingredient. 1,2 Colloidal NCs stabilized by organic surfactants have been shown to pose excellent building blocks for the design of synthetic MCs with tailored structural properties which are conveniently obtained by self-assembly of NCs from solution on a solid or liquid substrate by exploiting ligand-ligand 3 interactions. [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25] Typically, the utilized ligands consist of wide-gap, bulky hydrocarbons which render the MCs insulating. [26][27][28][29][30][31][32][33] MCs obtained in this way exhibit average grain sizes of ~150 µm 2 , which enables a detailed characterization by electron and/or X-ray microscopy. 34 Since the optoelectronic properties of PbS NC ensembles bear many opportunities for applications in solar cells or photodetectors, a number of ligand exchange procedures with small organic or inorganic molecules as well as single atom passivation strategies have been developed, all of which greatly increase the carrier mobilities within the SL of NCs. 28,33,[35][36][37][38][39][40][41][42][43][44] Due to the short interparticle spacing imposed by these ligands, structural coherence is mostly lost in such superlattices, but in rare cases it has been demonstrated that significant long-range order and even mesocrystallinity can be preserved. 25,35,45 However, a persisting problem of these protocols is that they are prone to introduce defects in the superlattice structure with some degree of granularity and signifi...

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.