Table 2. ARCIMBOLDO results for HTH proteins.
Results are shown for several approaches to solve the target structure 3RKQ (115 amino acids and 19 bp) with the fragment models. The TFZ, CC and MPE values in the case of a solution are given in bold. Results are shown after locating two fragments with Phaser.
| TFZ | CC (%) | MPE (°) | |
|---|---|---|---|
| Full models with DNA and protein with side chains (31–33 amino acids and 7–8 bp) | |||
| 1akh | 6.35 | 31.49 | 33.50 |
| 1au7 | 6.78 | 30.37 | 33.60 |
| 1b8i | 10.57 | 30.55 | 33.50 |
| 1du0 | 18.08 | 30.94 | 33.80 |
| 1fjl | 15.27 | 30.49 | 33.40 |
| 1gt0 | 7.01 | 8.83 | 90.20 |
| 1yrn | 14.88 | 30.66 | 33.70 |
| 2d5v | 11.84 | 31.01 | 33.90 |
| 2h1k | 18.07 | 31.93 | 33.50 |
| 2hdd | 15.20 | 30.45 | 33.60 |
| 2r5z | 12.46 | 30.19 | 34.00 |
| 9ant | 19.66 | 30.57 | 33.70 |
| Full models with DNA and protein without side chains (31–33 amino acids and 7–8 bp) | |||
| 1akh | 6.59 | 9.51 | 89.40 |
| 1au7 | 7.46 | 30.53 | 33.80 |
| 1b8i | 8.49 | 31.08 | 33.30 |
| 1du0 | 16.38 | 30.46 | 33.30 |
| 1fjl | 11.83 | 30.97 | 33.50 |
| 1gt0 | 7.32 | 9.96 | 89.00 |
| 1yrn | 10.69 | 31.05 | 33.70 |
| 2d5v | 12.13 | 31.48 | 33.40 |
| 2h1k | 14.63 | 30.23 | 33.40 |
| 2hdd | 10.87 | 31.01 | 33.40 |
| 2r5z | 11.46 | 30.86 | 34.00 |
| 9ant | 19.58 | 30.33 | 33.90 |
| Models without DNA, protein with side chains (31–33 amino acids) | |||
| 1akh | 10.58 | 30.00 | 34.20 |
| 1au7 | 6.33 | 10.74 | 88.90 |
| 1b8i | 13.22 | 30.95 | 33.70 |
| 1du0 | 6.51 | 11.27 | 73.60 |
| 1fjl | 6.62 | 9.94 | 89.50 |
| 1gt0 | 7.83 | 31.06 | 33.40 |
| 1yrn | 10.98 | 31.22 | 33.60 |
| 2d5v | 6.54 | 30.29 | 33.50 |
| 2h1k | 10.37 | 31.04 | 33.90 |
| 2hdd | 6.64 | 11.37 | 88.50 |
| 2r5z | 6.75 | 29.71 | 33.80 |
| 9ant | 11.51 | 30.64 | 34.10 |
| Models without DNA, protein without side chains (31–33 amino acids) | |||
| 1akh | 6.86 | 10.49 | 89.50 |
| 1au7 | 7.00 | 11.13 | 89.40 |
| 1b8i | 6.62 | 10.27 | 89.40 |
| 1du0 | 6.11 | 10.25 | 89.20 |
| 1fjl | 6.68 | 10.91 | 89.50 |
| 1gt0 | 8.79 | 31.34 | 33.30 |
| 1yrn | 7.07 | 10.71 | 89.70 |
| 2d5v | 6.84 | 11.06 | 89.30 |
| 2h1k | 6.35 | 10.44 | 89.10 |
| 2hdd | 6.49 | 11.07 | 89.50 |
| 2r5z | 7.74 | 10.24 | 89.10 |
| 9ant | 7.67 | 10.86 | 89.30 |
| Models with DNA, only one helix of the protein with side chains (15–17 amino acids and 7–8 bp) | |||
| 1akh | 7.29 | 31.33 | 33.30 |
| 1au7 | 8.05 | 30.96 | 33.60 |
| 1b8i | 8.85 | 30.45 | 33.90 |
| 1du0 | 16.02 | 30.46 | 33.40 |
| 1fjl | 8.10 | 30.27 | 33.30 |
| 1gt0 | 7.64 | 31.16 | 33.60 |
| 1yrn | 10.72 | 30.90 | 33.60 |
| 2d5v | 11.25 | 30.38 | 33.90 |
| 2h1k | 15.96 | 31.12 | 33.40 |
| 2hdd | 13.06 | 30.53 | 33.60 |
| 2r5z | 10.29 | 30.71 | 33.50 |
| 9ant | 15.90 | 30.57 | 33.60 |
| Models with DNA, only one helix of the protein without side chains (15–17 amino acids and 7–8 bp) | |||
| 1akh | 6.75 | 9.78 | 89.30 |
| 1au7 | 10.01 | 30.44 | 33.30 |
| 1b8i | 7.07 | 11.14 | 89.10 |
| 1du0 | 14.17 | 31.28 | 33.80 |
| 1fjl | 7.64 | 11.29 | 89.20 |
| 1gt0 | 7.18 | 9.77 | 89.60 |
| 1yrn | 6.98 | 9.82 | 89.40 |
| 2d5v | 11.20 | 30.96 | 33.70 |
| 2h1k | 11.45 | 30.92 | 33.50 |
| 2hdd | 10.02 | 29.89 | 34.10 |
| 2r5z | 7.91 | 30.73 | 33.50 |
| 9ant | 14.09 | 31.54 | 33.10 |
| Ideal helix (14 amino acids; after location of two fragments) | |||
| 8.69 | 31.43 | 33.20 | |