Table 1.
Crystallographic data collection and structure refinement statistics
The values in parentheses are for the highest-resolution shell. ASU, asymmetric unit; RMSD, root-mean-square deviation.
| Human alk-SMase with PC | Human alk-SMase | |
|---|---|---|
| PDB code | 5TCD | 5UDY |
| Data collection | ||
| Space group | P3121 | P3121 |
| Unit cell a, b, c (Å) | 104.22, 104.22, 113.89 | 103.25, 103.25, 113.55 |
| Unit cell α, β, γ (°) | 90, 90, 120 | 90, 90, 120 |
| X-ray wavelength (Å) | 0.9795 | 0.9795 |
| Resolution range (Å) | 50–2.40 (2.49–2.40) | 50–2.60 (2.69–2.60) |
| Total reflections | 155,404 (14,219) | 120,607 (11,858) |
| Unique reflections | 28,331 (2,788) | 21,834 (2,156) |
| Multiplicity | 5.5 (5.1) | 5.5 (5.5) |
| Completeness (%) | 100 (100) | 100 (100) |
| Rmeas (%) | 6 (113) | 7 (137) |
| Rpim (%) | 3 (44) | 4 (67) |
| Mean I/σ(I) | 25.8 (1.4) | 19.0 (1.1) |
| CC½ | (0.822) | (0.692) |
| Wilson B factor (Å2) | 31.0 | 38.1 |
| Refinement | ||
| Protein copies per ASU | 1 | 1 |
| Resolution range (Å) | 37.96–2.40 (2.49–2.40) | 35.12–2.60 (2.69–2.60) |
| Reflections used | 23,507 (948) | 18,878 (662) |
| Reflections for Rfree | 1,916 (86) | 1,532 (59) |
| Rwork (%) | 17.3 (23.6) | 17.9 (28.7) |
| Rfree (%) | 20.8 (27.4) | 20.9 (30.7) |
| Non-hydrogen atoms | 3,555 | 3,457 |
| Protein | 3,152 | 3,158 |
| Glycans, ligands, ions | 198 | 136 |
| Water | 205 | 163 |
| Average B factor (Å2) | 39.6 | 43.6 |
| Protein | 37.8 | 43.0 |
| Glycans, ligands, ions | 72.4 | 67.7 |
| Water | 35.8 | 34.6 |
| RMSD bond lengths (Å) | 0.003 | 0.004 |
| RMSD bond angles (°) | 0.60 | 0.72 |
| Ramachandran favored (%) | 96.1 | 97.9 |
| Ramachandran allowed (%) | 3.9 | 2.1 |
| Ramachandran outliers (%) | 0 | 0 |
| Clashscore | 1.1 | 1.4 |