 | Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
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![[Figure 9]](wd5176fig9mag.jpg)
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Figure 9
Normal and pathological side-chain density. 2 mFo − DFc electron density contoured at 0.8σ. The left panel shows the progressive weakening of electron density owing to displacement of the side-chain atoms, after re-refinement with the originally zero occupancies reset to 1. The B factors are restrained against unreasonable increases between subsequent adjacent atoms, and in normal situations show a continuous increase along the side chain. The right panel shows an improbable scenario where atoms that had previously zero occupancies assigned refine to extreme B factors at the limit of what the restraints allow and the electron density abruptly disappears, and, in the case of Lys130, abruptly reappears for the terminal C∊ and Nζ side chain atoms. This is also true but less visible owing to the stronger main-chain B-factor restrains for the Lys130 backbone O atom. These observations provide a first indication that the deposited structure factors do not to contain any contributions from the unoccupied atoms. Note that in some real scenarios the terminal lysine Nζ for example can be tethered through non-covalent interactions with inter- or intra-molecular neighboring residues and become better defined than the remaining hydrophobic side-chain atoms. This is however not the case for Lys130 of 3k78 . All density figures were prepared with XtalView (McRee, 1999  ) and rendered by Raster3d (Merritt & Bacon, 1997). |
![[Figure 9]](wd5176fig9.jpg)
| STRUCTURAL BIOLOGY COMMUNICATIONS |
ISSN: 2053-230X
