This PDF file includes:

• fig. S1. Radius distribution of gold nanocrystals.
  
• fig. S2. SAXS scattering profiles of end-labeled DNA samples for label position reconstruction.
  
• fig. S3. SAXS scattering profiles of the full set of DNA samples for internal label position reconstruction.
  
• fig. S4. SAXS scattering profiles of two end-labeled RNA kink-turn motif samples.
  
• fig. S5. SAXS data for unlabeled calmodulin.
  
• fig. S6. Pair-distance distributions for all unlabeled and labeled samples.
  
• fig. S7. SAXS scattering profiles of two different labeled calmodulin samples.
  
• fig. S8. Spread of the best-fitting position depending on the initial trial point density.
  
• table S1. DNA sequences used in the experiments on end-labeled DNA.
  
• table S2. DNA sequences used in the experiments with internally labeled DNA.
  
• table S3. RNA kink-turn sequence.
  
• table S4. Radii of gyration R_g values for all unlabeled and labeled samples.

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