TABLE 1.
Data collection and refinement statistics
Values in parentheses are for the highest resolution shell. r.m.s.d., root mean square deviation.
| Native APA | APA-glutamate complex | APA-Ca-glutamate complex | APA-Ca-aspartate complex | APA-arginine complex | APA-amastatin complex | APA-bestatin complex | |
|---|---|---|---|---|---|---|---|
| Data collection | |||||||
| Space group | P6422 | P6422 | P6422 | P6422 | P6422 | P6422 | P6422 |
| Cell dimensions | |||||||
| a, c (Å) | 142.3, 237.3 | 142.2, 237.1 | 142.2, 237.1 | 142.1, 237.4 | 142.3, 237.2 | 142.7, 237.8 | 141.9, 237.1 |
| γ | 120° | 120° | 120° | 120° | 120° | 120° | 120° |
| Resolution (Å) | 50–2.05 | 50–2.4 | 50–2.15 | 50–2.4 | 50–2.25 | 50–2.4 | 50–2.4 |
| Total reflections | 534,840 | 336,976 | 525,986 | 403,261 | 481,998 | 609,019 | 334,475 |
| Unique reflections | 76,159 | 49,269 | 74,275 | 54,380 | 67,214 | 53,672 | 55,096 |
| Wilson B-factor | 35.90 | 42.53 | 31.44 | 45.48 | 32.96 | 34.62 | 43.00 |
| Rsym | 0.080 (0.573) | 0.085 (0.537) | 0.083 (0.454) | 0.077 (0.613) | 0.095 (0.439) | 0.126 (0.425) | 0.086 (0.639) |
| Rp.i.m. (41, 42) | 0.035 (0.274) | 0.033 (0.264) | 0.031 (0.196) | 0.032 (0.271) | 0.038 (0.200) | 0.039 (0.131) | 0.038 (0.278) |
| I/σ | 22.0 (2.9) | 17.5 (2.6) | 19.16 (3.67) | 25.7 (2.3) | 21.8 (3.9) | 14.9 (7.18) | 21.4 (2.4) |
| Completeness (%) | 99.4 (99.6) | 88.7 (90.8) | 97.3 (93.9) | 97.9 (98.9) | 99.8 (98.3) | 98.2 (100.0) | 99.7 (99.7) |
| Redundancy | 6.0 (5.2) | 6.8 (5.1) | 7.0 (5.6) | 7.3 (7.1) | 7.1 (5.5) | 11.0 (10.5) | 6.0 (5.7) |
| Refinement | |||||||
| Resolution (Å) | 38.9–2.15 | 38.8–2.4 | 45.6–2.15 | 48.6–2.4 | 45.6–2.25 | 41.2–2.4 | 33.8–2.4 |
| Test set reflections | 3832 | 2518 | 3742 | 2750 | 3403 | 2713 | 2793 |
| Rwork/Rfree | 0.173/0.218 | 0.167/0.226 | 0.183/0.248 | 0.152/0.224 | 0.167/0.236 | 0.210/0.276 | 0.170/0.252 |
| No. of atoms | 7993 | 7854 | 7945 | 7901 | 8011 | 7956 | 7853 |
| Protein | 7186 | 7153 | 7159 | 7159 | 7160 | 7151 | 7159 |
| Carbohydrate | 210 | 238 | 224 | 224 | 224 | 238 | 224 |
| Ligand | 0 | 10 | 10 | 9 | 12 | 33 | 22 |
| Ion | 1 | 1 | 2 | 2 | 1 | 1 | 1 |
| Water | 595 | 452 | 550 | 507 | 614 | 533 | 445 |
| B-factors (Å2) | 58.7 | 61.5 | 56.9 | 64.6 | 59.7 | 56.1 | 65.4 |
| Protein | 56.9 | 59.6 | 55.2 | 62.8 | 57.5 | 54.2 | 63.6 |
| Ligand | 79.7 | 67.1 | 96.3 | 94.9 | 53.4 | 74.4 | |
| Ion | 80.8 | 74.1 | 59.2 | 77.0 | 85.0 | 76.5 | 74.2 |
| Water | 58.8 | 60.6 | 58.6 | 62.8 | 61.9 | 55.2 | 64.4 |
| r.m.s.d. | |||||||
| Bond lengths (Å) | 0.007 | 0.008 | 0.007 | 0.007 | 0.008 | 0.009 | 0.009 |
| Bond angles | 1.239° | 1.297° | 1.265° | 1.201° | 1.245° | 1.313° | 1.282° |
| Ramachandran plot | |||||||
| Favored (%) | 97 | 96 | 96 | 96 | 96 | 97 | 95 |
| Outliers (%) | 0.23 | 0.57 | 0.69 | 0.57 | 0.57 | 0.69 | 0.34 |