Table 1.
Crystal structure data collection and refinement statistics
| D402N NAO | D402N NAO | S276A NAO | Wild-type NAO | |
|---|---|---|---|---|
| PDB code | 3D9D | 3D9E | 3D9F | 3D9G |
| Substrate Ligand(s) | 1-NO2-hexane | 1-NO2-octane | 1-NO2-hexane | cyanide + 1-NO2-hexane |
| Wavelength (Å) | 1.1000 | 1.0809 | 0.9798 | 1.0809 |
| Space group | P3221 | P3221 | P3221 | P3221 |
| a (Å), b (Å), c (Å) | 107.9, 107.9, 338.4 | 108.0, 108.0, 338.6 | 108.3, 108.3, 339.4 | 109.3, 109.3, 343.9 |
| Resolution range (Å) | 49 - 2.10 | 49 - 2.20 | 49 - 2.20 | 49 - 2.15 |
| High resolution shell (Å) | 2.80 - 2.10 | 2.28 - 2.20 | 2.28 - 2.20 | 2.23 - 2.15 |
| Total observations | 391271 | 602598 | 490262 | 803662 |
| Unique observations | 123094 | 110228 | 115243 | 122023 |
| Completeness (%) | 91.9 (62.1)a | 93.8 (64.9) | 97.4 (83.2) | 94.2 (64.9) |
| Redundancy | 3.2 (1.6)a | 5.5 (2.4) | 4.3 (4.0) | 6.6 (1.8) |
| Rsym (%)b | 8.9 (44.7)a | 6.0 (43.4) | 6.9 (55.2) | 10.4 (28.5) |
| I / σ I | 13.7 (1.3)a | 23.2 (1.4) | 26.3 (2.2) | 27.4 (1.92) |
| Model refinement statistics | ||||
| Total number of non-hydrogen atoms | 14165 | 13772 | 13974 | 14353 |
| No. residues protein/ligand/water | 1724/16/650 | 1723/12/273 | 1722/16/468 | 1721/6/840 |
| Resolution range (Å) | 50 - 2.1 | 50 - 2.2 | 50 - 2.2 | 50 - 2.15 |
| No. of reflections | 116861 | 104709 | 109423 | 115721 |
| Rcryst (%)c | 18.0 (26.7)a | 19.3 (27.4)a | 20.2 (27.0)a | 19.6 (24.3)a |
| Rfree (%)d | 21.9 (32.7)a | 23.3 (33.7)a | 24.1 (30.5)a | 23.3 (30.2)a |
| Estimated overall coordinate error based on R-value (Å) | 0.192 | 0.232 | 0.231 | 0.216 |
| Correlation coefficient (Fo - Fc) | 0.957 | 0.956 | 0.955 | 0.954 |
| Ramachandran statistics | ||||
| Most favored | 1377 (91.5%) | 1399 (92.8%) | 1377 (91.6%) | 1394 (92.6%) |
| Additional allowed | 118 (7.8%) | 100 (6.6%) | 117 (7.7%) | 103 (6.8%) |
| Generously allowed | 4 (0.3%) | 4 (0.3%) | 6 (0.4%) | 3 (0.2%) |
| Disallowed | 6 (0.4%) | 4 (0.3%) | 4 (0.3%) | 5 (0.3%) |
| Average B values (Å2) | ||||
| Protein | 36.07 | 42.2 | 44.0 | 38.0 |
| Water | 38.8 | 38.4 | 43.0 | 40.8 |
| Substrate ligand | 50.2 | 60.2 | 55.2 | -- |
| FAD | 29.7 | 34.4 | 38.7 | 32.2 |
| R.m.s.d. from ideal geometry | ||||
| Bond lengths (Å) | 0.014 | 0.011 | 0.012 | 0.010 |
| Bond angles (˚) | 1.53 | 1.35 | 1.35 | 1.30 |
a
Highest resolution shell.
b
Σ(|Ihkl - <Ihkl>|) / Σ Ihkl
c
R-value calculated with the working and the test set inclusive.
d
Free R-value test set calculated with 5% of the data.