The E. coli LPS structure included here was generated using CHARMM-GUI's LPS Modeler with Type 1 Lipid A, an R1 core, and 8 O11-antigen repeats. Additional details for this structure can be found in Lee and Dommer et al. The laminarin oligosaccharide model was constructed using the CHARMM-GUI glycan modeler. Laminarin naturally contains a variety of molecular weights and branching ratios, complexity which is nearly impossible to recreate computationally. However, given the small size of our systems and the high variability across single particles, we opted to create one laminarin structure to represent neutral, branched oligosaccharides. Thus, a polymeric structure of a molecular weight between that of free glucose and the LPS model was generated with 15 glucose monomers, linked together with 𝛽(1à3) linkages, with branches incorporated at monomers 3 and 9 by 𝛽(1à6) linkages (Figure ). The structure of BCL (PDB ID: 3LIP) was prepared for a pH 5 environment using NAMD Psfgen. The number of water molecules was calculated based on an estimated relative humidity for the particles of 70-80%, amounting to ~50% water by mass. All molecular structures were randomly packed into 16 geometrically distinct segments (to later combine into a sphere) using PACKMOL 100 in 3 successive rounds of packing. The most difficult structures to place (macromolecular structures BCL, laminarin, and LPS) were packed first, followed by small molecules including FAs and glucose, and finally ions and TIP3P 101,102 water. Small fluctuations in the random seed in the PACKMOL packing algorithm introduced subtle differences in the number and locations of each ingredient placed for each of the packed segments. Thus, the initial molecular configurations between replicates of the same system contain small random variations and reflect variations one might find between particles when doing single particle analysis.