Table 1.
X-ray diffraction data collection and refinement statistics
| Ligands | Ca2+, ATP | Kanamycin, SP600125 | Kanamycin, PP1 | Kanamycin, PP2 | Kanamycin, Tyrphostin AG 1478 | Kanamycin, 1-NA-PP1 | Kanamycin, 1-NM-PP1 |
|---|---|---|---|---|---|---|---|
| PDB Code | 4EJ7 | 4FEU | 4FEV | 4FEW | 4FEX | 4GKH | 4GKI |
| Data collection | |||||||
| Space group Cell dimensions | C2221 | P1 | P1 | P1 | P1 | P1 | P1 |
| a, b, c, Å | 85.4, 152.5, 165.6 | 57.8, 94.2, 96.8 | 57.6, 94.2, 96.9 | 57.3, 93.6, 96.4 | 57.7, 93.7, 96.3 | 97.2, 97.3, 112.7 | 96.8, 97.1, 112.1 |
| α, β, γ, ° | 90, 90, 90 | 61.2, 73.1, 87.4 | 61.1, 73.1, 87.4 | 61.2, 73.2, 87.4 | 118.8, 103.6, 93.4 | 103.0, 106.2, 112.7 | 103.2, 106.2, 112.7 |
| Resolution, Å | 43.7 – 2.29 | 20.0 – 2.37 | 20.0 – 1.89 | 24.00 – 1.98 | 20.0 – 2.71 | 80.87 – 1.86 | 99.63 – 1.88 |
| Rsyma | 0.090 (0.530)b | 0.072 (0.423) | 0.047 (0.337) | 0.068 (0.405) | 0.061 (0.562) | 0.061 (0.401) | 0.062 (0.372) |
| I / σ(I) | 12.55 (1.50) | 16.35 (2.00) | 27.48 (3.02) | 19.26 (2.15) | 19.39 (2.04) | 11.1 (2.8) | 7.6 (2.1) |
| Completeness, % | 91.9 (69.4) | 98.4 (98.4) | 97.8 (96.5) | 98.1 (96.7) | 98.9 (98.5) | 97.2 (96.5) | 97.6 (96.5) |
| Redundancy | 5.7 (5.8) | 2.7 (2.7) | 3.1 (3.1) | 3.1 (3.1) | 3.9 (3.9) | 3.9 (3.9) | 2.3 (2.3) |
| Refinement | |||||||
| Resolution, Å | 43.67 – 2.40 | 20.0 – 2.37 | 19.97 – 1.89 | 23.90 – 1.98 | 19.9 – 2.69 | 54.78 – 1.86 | 54.38 – 1.88 |
| No. of reflections: working, test | 71660, 3148 | 67481, 3406 | 128187, 1972 | 111054, 5461 | 45056, 1939 | 275305, 13290 | 257334, 12522 |
| R-factor/free R-factorc | 21.5/25.2 (32.0/34.5) | 16.0/21.5 (18.8/21.8) | 15.4/20.4 (20.3/27.1) | 15.7/21.6 (25.1/34.0) | 18.4/24.0 (30.4/37.8) | 16.4/21.6 (25.8/28.9) | 16.6/21.6 (28.5/33.5) |
| No. of refined atoms, molecules | |||||||
| Protein | 6402, 3 | 12085, 6 | 12750 | 12422 | 10409, 5 | 25109, 12 | 25260, 12 |
| Kanamycin | 105 | 198, 6 | 198, 6 | 198, 6 | 165, 5 | 396, 12 | 396, 12 |
| Inhibitor | N/A | 51, 3 | 146, 6 | 147, 6 | 88, 4 | 288, 12 | 300, 12 |
| Solvent | 7 | 24 | 11 | 46 | 7 | 181 | 169 |
| Water | 302 | 685 | 1412 | 1190 | 178 | 2868 | 3307 |
| B-factors | |||||||
| Protein | 43.7 | 56.4 | 24.8 | 35.9 | 54.0 | 48.5 | 37.0 |
| Kanamycin | 41.1 | 48.7 | 17.3 | 26.6 | 43.8 | 38.6 | 26.7 |
| Ca2+, ATP | 46.7, 40.4 | N/A | N/A | N/A | N/A | N/A | N/A |
| Inhibitor | N/A | 52.0 | 28.0 | 36.7 | 66.9 | 52.1 | 48.3 |
| Solvent | 55.8 | 80.7 | 17.3 | 57.4 | 63.4 | 70.4 | 65.5 |
| Water | 41.3 | 48.4 | 29.2 | 35.7 | 42.9 | 49.5 | 37.7 |
| R.m.s.d. | |||||||
| Bond lengths, Å | 0.009 | 0.010 | 0.007 | 0.009 | 0.010 | 0.009 | 0.008 |
| Bond angles, ° | 0.694 | 1.07 | 1.13 | 1.14 | 1.30 | 1.173 | 1.159 |
a
Rsym = ΣhΣi|Ii(h) - 〈I(h)〉/ΣhΣiIi(h), where Ii(h) and 〈I(h)〉 are the ith and mean measurement of the intensity of reflection h.
b
Figures in parentheses indicate the values for the outer shells of the data.
c
R = Σ|Fpobs – Fpcalc|/ΣFpobs, where Fpobs and Fpcalc are the observed and calculated structure factor amplitudes, respectively.