Table 2. Application of iterative statistical density modification with local pattern recognition.
For each experimental data set, density modification was carried out using default inputs for RESOLVE (Terwilliger, 2000) and phase probabilities calculated using SOLVE (Terwilliger & Berendzen, 1999). The process shown in Fig. 1 ▶ was then carried out, including the identification and use of local patterns of density. Non-crystallographic symmetry was not included in any density-modification procedures in these tests. The correlation coefficient of the resulting electron-density maps to those calculated with phases obtained from the refined models of each structure are listed. Additionally, the number of residues that could be automatically modeled and assigned to sequence and the number that could be modeled (whether or not assigned to sequence) with RESOLVE (Terwilliger, 2003a ▶,b ▶) using default parameters are listed. As the number of residues obtained with automated model building is somewhat sensitive to the parameters and details of the methods used, models were built with versions 2.02, 2.03, 2.04 and 2.05 of RESOLVE and the average numbers of residues built are reported.
| Structure | UTP-synthase† | Armadillo repeat of β-catenin‡ | Gene 5 protein§ | Hypothetical (P. aerophilum ORF)¶ | NusA†† | NDP-kinase‡‡ |
|---|---|---|---|---|---|---|
| Resolution (Å) | 2.8 | 2.7 | 2.6 | 2.6 | 2.4 | 2.4 |
| Type of experiment | SAD | MAD | MAD | MAD | SAD | MAD |
| RESOLVE map correlation to model map | ||||||
| With local patterns | 0.760 | 0.874 | 0.815 | 0.821 | 0.847 | 0.649 |
| Without local patterns | 0.727 | 0.872 | 0.786 | 0.811 | 0.648 | 0.586 |
| Residues in refined model | 1012 (2 × 506) | 455 | 86 | 494 (2 × 247) | 344 | 556 (3 × 186) |
| Main-chain residues built by RESOLVE (%) | ||||||
| With local patterns | 72 | 78 | 72 | 76 | 56 | 76 |
| Without local patterns | 72 | 78 | 69 | 76 | 49 | 76 |
| Side-chain residues built by RESOLVE (%) | ||||||
| With local patterns | 34 | 58 | 52 | 65 | 21 | 18 |
| Without local patterns | 24 | 58 | 51 | 61 | 5 | 4 |