TABLE 1.
Refinement statistics
| APH(9)-Ia | APH(9)-Ia + AMP | APH(9)-Ia + ADP + spectinomycin | |
|---|---|---|---|
| Resolution range (Å) | 50–1.7 | 50–2.8 | 50–2.4 |
| Space group | P21 | P3121 | P3121 |
| a (Å) | 47.41 | 74.47 | 75.01 |
| b (Å) | 70.70 | ||
| c (Å) | 99.31 | 135.5 | 139.9 |
| b (°) | 95.93 | ||
| Number of reflections | |||
| Working set | 57720 | 8766 | 15505 |
| Test set | 6473 | 998 | 1661 |
| Rcrysta/Rfreeb | 0.182/0.228 | 0.265/0.346 | 0.230/0.277 |
| Number of non-hydrogen atoms | |||
| Protein | 5589 | 2640 | 2615 |
| Cofactor | 23 | 27 | |
| Ion | 1 Ni2+ | 1 Ni2+/1 Mg2+ | |
| Substrate | 24 | ||
| Solvent | 860 | 16 | 48 |
| Root mean square deviation | |||
| Bond length (Å) | 0.010 | 0.008 | 0.007 |
| Bond angles (°) | 1.40 | 1.40 | 1.30 |
| Average thermal factor (Å2) | |||
| Protein | 22.02 | 62.89 | 53.41 |
| Cofactor | 62.70 | 54.02 | |
| Ion | 55.69 | 51.36 | |
| Substrate | 34.42 | ||
| Solvent | 37.97 | 48.45 | 42.22 |
| Ramachandran plotc (%) | |||
| Most favored regions | 91.0 | 78.8 | 86.4 |
| Additional allowed regions | 8.1 | 19.1 | 13.2 |
| Generously allowed regions | 0.7 | 1.8 | 0.3 |
| Disallowed regions | 0.2 | 0.4 | 0 |
a Rcryst = Σ (|Fo| − |Fc|)/Σ|Fo|, where |Fo| is the observed and |Fc| is the calculated structure factor amplitude of a reflection.
b Rfree was calculated by randomly omitting 10% of the observed reflections from the refinement.
c According to the Ramachandran plot in PROCHECK (61).