A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme

MacElrevey, C.; Spitale, R.C.; Krucinska, J.; Wedekind, J.E.

doi:10.1107/S090744490702464X

Figure 5
Schematic surface and ball-and-stick diagrams illustrating the 6₁ packing interactions of hinged hairpin-ribozyme constructs. (a) Comparison of C3L (blue) and S9L (magenta) unit cells. The perspective represents the interaction of molecules about the 6₁ screw axis. (For twofold and 2₁ operations, refer to Fig. 6

a.) Superposition of C3L onto S9L initiates at the third molecule from the bottom (i.e. the `reference' molecule), represented in bold magenta and blue overlay. Symmetry operations used to generate the remaining molecules demonstrate the degeneration of the superposition as a result of the 15 Å elongated unit cell of the C3L structure. C3L molecules are shown in blue and green, with S9L structures shown in pink. The dashed box denotes the inset for (b) and (c). (b) Expanded view of the 6₁ packing scheme for the S9L structure. Atoms engaged in potential hydrogen bonds are depicted as white spheres. Helices are labeled as in Fig. 1

(c) and primes (′) denote symmetry-related molecules. An additional H3′′ helix that is packed in a blunt-ended base stack with H4 has been omitted for clarity. The asymmetric unit (H4) is colored magenta, with symmetry molecules in red (H3′) or light pink (H4′). (c) The C3L 6₁ packing scheme as described in (b), but the asymmetric unit is colored blue and symmetry mates are coloured teal (H3′) or green (H4′). White spheres identify equivalent atoms in the C3L structure that are engaged in hydrogen bonding in the S9L structure. (d)–(g) Detailed view of hydrogen-bond interactions with each of four H4 residues. The A31 and U31 residues are base-paired; A31 ends the linker strand, while U31 begins the S-turn strand. (h)–(k) Equivalent distances in the C3L structure demonstrate the loss of 6₁-fold packing interactions.

BIOLOGICAL
CRYSTALLOGRAPHY

ISSN: 1399-0047

Volume 63| Part 7| June 2007| Pages 812-825

doi:10.1107/S090744490702464X

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