Table 2. Comparison of three methods in re-refining 16 low-resolution structures.
The results of refining 16 low-resolution structures. R free and its improvement, R free R work, as well as Ramachandran statistics, are shown. Statistically, of the total of 16 test systems, DCN outperformed DEN in 16 cases (100%) with respect to R free, 16 (100%) with respect to R free R work and 13 (81.25%) with respect to Ramachandran statistics. When compared with conventional refinement, these ratios became 100, 87.5 and 93.75%, respectively. The properties of the structure, the experimental data and the reference model for each test system are listed in Supplementary Tables S1 and S2.
| R free (%) | DCN improvement (%) | R free R work (%) | Ramachandran statistics | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PDB code | Resolution () | Conventional | DEN | DCN | R free over conventional | R free over DEN | Conventional | DEN | DCN | Conventional | DEN | DCN | DCN conventional | DCN DEN |
| 1isr | 4.00 | 22.37 | 21.64 | 21.10 | 1.27 | 0.54 | 6.6 | 6.4 | 6.1 | 0.833 | 0.863 | 0.878 | 0.045 | 0.015 |
| 1jl4 | 4.30 | 37.00 | 36.39 | 35.25 | 1.75 | 1.14 | 10.9 | 11.5 | 11.1 | 0.567 | 0.712 | 0.718 | 0.151 | 0.006 |
| 1r5u | 4.50 | 31.65 | 30.48 | 29.83 | 1.82 | 0.65 | 5.6 | 5.2 | 4.8 | 0.646 | 0.730 | 0.748 | 0.102 | 0.018 |
| 1xxi | 4.10 | 38.21 | 32.24 | 31.46 | 6.75 | 0.78 | 11.2 | 9.9 | 9.4 | 0.631 | 0.806 | 0.800 | 0.169 | 0.006 |
| 1ye1 | 4.50 | 33.77 | 30.24 | 29.36 | 4.41 | 0.88 | 13.8 | 13.1 | 12.5 | 0.781 | 0.853 | 0.905 | 0.124 | 0.052 |
| 1ym7 | 4.50 | 27.64 | 27.39 | 27.23 | 0.41 | 0.16 | 3.0 | 3.4 | 3.3 | 0.703 | 0.781 | 0.751 | 0.048 | 0.030 |
| 2a62 | 4.50 | 36.22 | 35.48 | 33.53 | 2.69 | 1.95 | 9.6 | 8.6 | 6.9 | 0.568 | 0.651 | 0.670 | 0.102 | 0.019 |
| 2bf1 | 4.00 | 48.66 | 44.31 | 42.66 | 6.00 | 1.65 | 8.6 | 5.0 | 4.0 | 0.383 | 0.453 | 0.523 | 0.140 | 0.070 |
| 2i37 | 4.15 | 36.46 | 33.20 | 32.57 | 3.89 | 0.63 | 3.7 | 1.2 | 0.3 | 0.737 | 0.851 | 0.848 | 0.111 | 0.003 |
| 2q7n | 4.00 | 26.49 | 26.21 | 26.06 | 0.43 | 0.15 | 2.1 | 1.9 | 1.8 | 0.774 | 0.768 | 0.770 | 0.004 | 0.002 |
| 2qag | 4.00 | 40.52 | 38.81 | 38.52 | 2.00 | 0.29 | 3.0 | 2.2 | 2.0 | 0.483 | 0.551 | 0.573 | 0.090 | 0.022 |
| 2vkz | 4.00 | 31.17 | 29.88 | 29.64 | 1.53 | 0.24 | 8.1 | 8.1 | 8.0 | 0.723 | 0.822 | 0.830 | 0.107 | 0.008 |
| 2yhj | 4.00 | 37.34 | 35.73 | 34.42 | 2.92 | 1.31 | 9.5 | 8.6 | 8.2 | 0.728 | 0.746 | 0.836 | 0.108 | 0.090 |
| 3alz | 4.51 | 25.01 | 24.61 | 23.67 | 1.34 | 0.94 | 1.9 | 1.6 | 0.9 | 0.667 | 0.712 | 0.721 | 0.054 | 0.009 |
| 3fus | 4.00 | 41.87 | 40.57 | 40.07 | 1.80 | 0.50 | 5.9 | 4.4 | 3.9 | 0.537 | 0.563 | 0.576 | 0.039 | 0.013 |
| 3us2 | 4.20 | 45.97 | 43.11 | 42.39 | 3.58 | 0.72 | 12.9 | 10.9 | 9.8 | 0.399 | 0.543 | 0.555 | 0.156 | 0.012 |
| Average | 4.20 | 35.02 | 33.14 | 32.36 | 2.66 | 0.78 | 7.3 | 6.4 | 5.8 | 0.635 | 0.713 | 0.731 | 0.096 | 0.019 |
| Minimum | 4.00 | 22.37 | 21.64 | 21.10 | 0.41 | 0.15 | 1.9 | 1.2 | 0.3 | 0.383 | 0.453 | 0.523 | 0.004 | 0.030 |
| Maximum | 4.51 | 48.66 | 44.31 | 42.66 | 6.75 | 1.95 | 13.8 | 13.1 | 12.5 | 0.833 | 0.863 | 0.905 | 0.169 | 0.090 |