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Figure 6
At high resolution, Cβ deviation outliers are most often due to problems with alternate conformations. (a) Amber refinement using the original Ser215 alternates in PDB entry 1nLs, which have widely separated positions for Cβ but only a single Cα atom. (b) Amber refinement after the definition of alternates has been spread to include the Cα and both adjoining peptides. (c) Amber refinement of the original Thr196 of PDB entry 1nLs, where alternate B had been fitted backwards; there is bad covalent geometry and a huge Cβd of 0.88 Å (sphere not shown). (d) The good Amber result after alternate B was refitted in the correct rotamer so that all atoms match the density.

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