TABLE 3.
Summary of diffraction data and structure refinement statistics
|
Caspase-3
|
||||
|---|---|---|---|---|
| Compound I | Compound II | Compound III | Compound IV | |
| Statistics of diffraction data | ||||
| Wavelength (Å) | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| Resolution range (Å)a | 50.0–2.50 (2.59–2.50) | 50.0–2.80 (2.90–2.80) | 50.0–2.60 (2.69–2.60) | 50.0–2.40 (2.49–2.40) |
| Space group | P212121 | P212121 | P212121 | P212121 |
| Cell parameters | ||||
| a (Å) | 65.1 | 65.7 | 65.4 | 65.2 |
| b (Å) | 96.9 | 96.5 | 96.7 | 96.3 |
| c (Å) | 180.4 | 180.5 | 180.4 | 180.2 |
| Observed reflections | 180,300 | 137,332 | 156,710 | 196,328 |
| Unique reflections | 36,312 | 27,196 | 35,800 | 41,447 |
| Average redundancy | 5.0 (4.7) | 5.0 (4.7) | 4.4 (3.0) | 4.7 (2.9) |
| Average I/σ(I) | 13.9 (2.0) | 15.0 (1.9) | 13.2 (1.3) | 17.1 (1.8) |
| Completeness (%) | 90.1 (70.8) | 94.3 (94.7) | 99.2 (94.1) | 91.5 (90.8) |
| Rmerge (%)b | 11.4 (43.5) | 12.8 (53.0) | 12.1 (48.2) | 9.1 (39.6) |
| Statistics of refinement | ||||
| Number of reflections | 36,280 | 27,133 | 35,739 | 41,413 |
| Working set | 34,487 | 25,767 | 33,954 | 39,360 |
| Free R set | 1,793 | 1,366 | 1,785 | 2,053 |
| R factor (%)c | 20.8 | 21.1 | 21.4 | 20.9 |
| Free R factor (%) | 26.8 | 29.1 | 27.4 | 25.3 |
| Number of residues | 930 | 933 | 930 | 936 |
| Number of water molecules | 181 | 74 | 124 | 241 |
| Average B factor of all atoms (Å2) | 59.9 | 72.4 | 61.7 | 56.3 |
| Caspase-3 | 60.0 | 72.6 | 61.9 | 56.4 |
| Inhibitor | 48.8 | 63.0 | 50.6 | 48.5 |
| Water molecule | 55.4 | 53.8 | 50.7 | 53.7 |
| r.m.s. deviationd bond lengths (Å) | 0.010 | 0.012 | 0.010 | 0.009 |
| r.m.s. deviation bond angles (°) | 1.2 | 1.4 | 1.2 | 1.2 |
| Ramachandran plot (%) | ||||
| Ramachandran favored | 96.3 | 95.3 | 96.5 | 97.2 |
| Ramachandran allowed | 99.7 | 99.6 | 99.6 | 99.8 |
| Ramachandran outliers | 0.3 | 0.4 | 0.4 | 0.2 |
Numbers in parentheses refer to the highest resolution shell
Rmerge = ΣhklΣi|Ii(hkl)i – 〈I(hkl)〉|/ΣhklΣiIi(hkl)
Rfactor = Σhkl||Fo| – |Fc||/Σhkl|Fo|
r.m.s. deviation, root mean square deviation