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Figure 11
HTH target 3RKQ . On the left side the search models are shown. The right side shows the Phaser and SHELXE results. Attempts in which ARCIMBOLDO succeeds in solving the PDB entry 3RKQ target are shown as green SHELXE CC (correlation coefficient) values (fragment PDB codes are listed at the bottom); the Phaser TFZ is plotted as blue squares. (a) Structure of the target 3RKQ (grey) with all of the models superimposed (coloured). (b) HTH fragments without truncation (31–33 amino acids, 7–8 bp); all but one (1gt0 ) solve the target structure 3RKQ . (c) HTH fragments with same number of residues as in (a) but with all side chains set to polyalanine; all models except 1akh and 1gt0 solve the target structure. (d) HTH fragments without DNA but with the full protein fragment; reducing the phasing information to HTH fragments reduces the number of successful solutions. (e) The same HTH fragments as in (d) but with polyalanines; one two-helix bundle HTH fragment with polyalanine side chains only solves in the case of 1gt0 . (f) Models with DNA but only one helix of the protein (the DNA-binding helix); all models can solve the target. (g) The same HTH fragments as in (f) but polyalanine; without the side chains not all models solve the target structure. The smallest solving fragment represents 3.82% of the mass of the asymmetric unit.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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