journal menu
![[Figure 2]](ei5112fig2mag.jpg)
|
|
Figure 2
MatchMaps results for poorly isomorphous DHFR data sets. (a) The structures 1rx2 and 1rx4 are similar overall (gray cartoons). The structures differ mainly at the active-site loop (1rx2, red cartoon; 1rx4, blue cartoon) and in the positions of the active-site ligands (1rx2, red sticks; 1rx4, blue sticks). (b) The same as panel (a), but rotated 90° to the right about the vertical axis (indicated). The side chain for phenylalanine 103 is shown as dark-gray sticks. (c) The unit cells of 1rx2 and 1rx4 differ by 2% along the longest dimension (left to right in this figure) from 98.912 to 100.879 Å. (d)–(f) Visualizations of the change in ligand position between 1rx2 (red sticks) and 1rx4 [(f), blue sticks]. Positive difference density is shown as a blue mesh and negative difference density as a red mesh. Importantly, the 1rx4 structural coordinates were not used in the creation of the isomorphous or MatchMaps maps. The isomorphous difference map contains essentially no interpretable signal. In contrast, the MatchMaps map in panels (e) and (f) contains clear signal for disappearance of the cofactor and lateral sliding of the substrate. There is also faint positive signal associated with the `swung-out' ribose ring, seen on the far left of the panel. Panel (f) is the same as panel (e), with the addition of the 1rx4 structural coordinates as blue sticks. (g)–(i) Visualizations of the change in loop conformation between 1rx2 and 1rx4. Only protein residues 21–25 are shown. Coloring is as in panels (d)–(f). (g) Again, the isomorphous difference map is not interpretable. (h) and (i) The MatchMaps positive difference density clearly corresponds to the 1rx4 structural model, which was not used in the creation of the map. Panel (i) is the same as panel (h), with the addition of the 1rx4 structural coordinates as blue sticks. (j) and (k) The impact of a spurious conformer on Fo–Fc and MatchMaps maps, respectively. The 1rx2 model for residues 101–105 is shown as red sticks. The spurious conformer for Phe103 is shown as gray sticks. (j) The Fo–Fc map shows clear positive (blue) and negative (red) density, recognizing the erroneous conformer as a conformational change. (k) MatchMaps does not show difference density for the spurious conformer. |
![[Figure 2]](ei5112fig2.jpg)
 | JOURNAL OF APPLIED CRYSTALLOGRAPHY |
ISSN: 1600-5767
access
