TABLE 1.
X-ray data collection and refinement statistics
| Apo-ecarpholin S | Ecarpholin S-lauric acid complex | Ecarpholin S-suramin complex | |
|---|---|---|---|
| Data collection | |||
| Cell parameters (Å) | a = 34.23, b = 39.48, c = 68.94 | a = b = 62.09, c = 124.25 | a = 51.45, b = 132.25, c = 86.10; β = 99.32 |
| Space group | P212121 | P3121 | P21 |
| Molecules/asymmetry unit | 1 | 2 | 8 |
| Resolution range (Å) | 50–2.0 | 50–1.95 | 50–2.2 |
| Wavelength (Å) | 1.5418 | 0.97 | 1.5418 |
| Observed reflections | 32,276 | 214,445 | 186,658 |
| Unique reflections | 6,463 | 20,851 | 55.923 |
| Completeness (%) | 95.7 (87.4) | 99.7 (100) | 97.5 (86.6) |
| Rsym (%)* | 0.051 | 0.050 | 0.089 |
| I/σ (I) | 24.7 (9.1) | 21.5 (2.4) | 10.8 (2.3) |
| Refinement and quality | |||
| Resolution range (Å) | 20–2.0 | 30–1.95 | 30–2.3 |
| Rwork (%)† | 19.2 | 22.8 | 21.7 |
| Rfree (%)‡ | 25.5 | 26.8 | 27.5 |
| rmsd bond lengths (Å) | 0.005 | 0.006 | 0.013 |
| rmsd bond angles(deg) | 1.3 | 1.3 | 1.6 |
| Average B-factors (Å2)§ | 30.5 | 29.1 | 33.7 |
| Main-chain | 28.4 | 26.3 | 31.9 |
| Side-chains | 31.3 | 30.0 | 33.2 |
| Waters | 38.0 | 35.4 | 32.0 |
| Lauric acid | 50.2 | ||
| Suramin chains | 36.4 | ||
| Ramachandran plot (%) | |||
| Most favored regions | 90.4 | 89.4 | 85.9 |
| Additional allowed regions | 9.6 | 10.6 | 13.9 |
| Generously allowed regions | 0 | 0 | 0.1 |
| Disallowed regions | 0 | 0 | 0 |
| Number of protein atoms | 959 | 1918 | 7672 |
| Number of ligand atoms | 0 | 28 | 1031 |
| Number of waters | 96 | 243 | 370 |
| Protein Data Bank code | 2QHE | 2QHD | 3BJW |
*
Rsym = ∑|Ii − 〈I〉|/∑|I|, where Ii is the intensity of the ith measurement, and 〈I〉 is the mean intensity for that reflection.
†
Rwork = ∑|Fobs–Fcalc|/∑|Fobs |, where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively.
‡
Rfree = Rwork, but for 10% of the total reflections randomly selected and omitted from refinement.
§
Individual B-factor refinement was performed.