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Figure 1
Single features (e.g. 10 nm protein, helix exposed to solvent, CH3 group, Zn atom) are shown in orange. Paired features (e.g. helix:helix, C≡C triple bond) are shown in blue. The contrast (in electrons) for paired features is given by the total number of electrons (e.g. 12 electrons for a C:C pair). This could be divided by a factor of 2 if one is interested in observing each component independently. When distinguishing between features (e.g. Zn and Fe, Tyr and Phe, or a protein surrounded by water), the difference in the number of electrons is relevant and the minus sign is used (e.g. Zn–Fe). For single features, the voxel size is given by the cube root of the atomic, group or molecular volume (as stated in Section 4[link], the atomic volume is a rather poor approximation for deriving the electron density distribution of an atom). For paired features it is given by the distance between the individual features. The straight line gives the contrast for different size proteins in a vacuum. Density values for cellular components are adapted from the work by Nave (2018BB10). See Table S1 of the supporting information from which all values were derived.

IUCrJ
Volume 10| Part 5| September 2023| Pages 603-609
ISSN: 2052-2525
https://doi.org/10.1107/S205225252300698X