Calculating Hydrodynamic and Geometric Properties of DENSS Electron Density Models

To calculate the hydrodynamic and geometric properties of the DENSS electron density models, we first cut the electron density volume to the support volume reported by DENSS by setting the electron density outside the support volume to 0. The support volume marks the upper limit of the particle volume. The support volume was then filled with the expected numbers of electrons (26376 for monomeric NET1ΔC, 52752 for dimeric NET1ΔC, 131800 for the NET1ΔC associated with heparin dp8/dp10 oligosaccharides). To estimate the real particle volume, we used the ATSAS suite to build bead models^{97 (link)}. We first generated two unique cores (damstart.pdb), each averaged^{98 (link)} from a set of 20 different (random seed) DAMMMIF models^{99 (link)}. The shape setting parameter suggested by DAMMIF was used for the 1^st core and the “unknown” shape setting parameter for the 2^nd core. From the 2 cores we calculated 4 DAMMIN models using different random seeds^{100 (link)}. The average volume of the 4 DAMMIN models was used as target volume for the hydrodynamic calculations. If the DAMMIN volume was larger than the average DENSS support volume, we used the latter, instead. We then proceeded with the programme HYDROMIC to calculate the hydrodynamic and geometric properties of the DENSS electron density models^{101 (link)}. For each dataset we had generated a set of 25 separate DENSS models (see SEC-SAXS section). For each set we provided a common electron density cut-off level to HYDROMIC, such that the resulting average volume of the entire set matched the target volume. We also calculated these properties for the averaged electron density map. The values for the averaged map and spread of the values for the refined models in brackets are given in Supplementary Table 5. We also included the properties of the DAMMIN bead models that were calculated using the programme HYDROPRO using the procedure we published earlier^{87 (link),102 (link)}. To accomplish the electron density volume calculations and manipulations we wrote Python scripts that were based on the saxstats module in DENSS^{30 (link)} and the volumeInfo and volumeViewer module from UCSF Chimera^{68 (link)}. The scripts are available from the authors on request.