TABLE 1.
Data collection and refinement statistics. Numbers in parentheses refer to the highest resolution shell. Rmerge = Σhkl Σi|Ihkl,i – 〈Ihkl〉|/Σhkl〈Ihkl〉; Rcryst and Rfree = (Σ||Fo| – |Fc||)/(Σ|Fo|); Rfactor and Rfree = (Σ||Fo| – |Fc||)/(Σ|Fo|).
| Crystal | Ligand free | Neu5Ac | Neu5Ac2en | Covalent intermediate |
|---|---|---|---|---|
| Data collection | ||||
| Space group and cell dimensions | P212121 | P212121 | P212121 | P21 |
| a = 96.9 Å, b = 69.0 Å, c = 72.8 Å | a = 97.0 Å, b = 69.4 Å, c = 72.7 Å | a = 98.9Å, b = 69.4Å, c = 71.0Å | a = 69.6Å, b = 97.4Å, c = 72.6Å, β = 91.0° | |
| X-ray source | ESRF ID14-1 | ESRF ID14-1 | ESRF ID14-2 | ESRF ID14-2 |
| Wavelength | 0.934 Å | 0.934 Å | 0.934 | 0.934 |
| Resolution | 20.0-0.97 Å (1.02-0.97 Å) | 20.0-0.97 Å (1.03-0.97 Å) | 28.4-1.50 (1.54-1.50) | 72.5-1.20 (1.27-1.20) |
| Unique reflections | 281,317 | 264,973 | 73,189 | 278,102 |
| Completeness | 98% (95%) | 92% (87%) | 93 (89) | 92 (85) |
| Redundancy | 4.6 (3.1) | 3.8 (3.1) | 3.4 (2.1) | 2.4 (2.2) |
| Rmerge | 0.072 (0.329) | 0.095 (0.186) | 0.055 (0.285) | 0.042 (0.304) |
| I/σI | 15.6 (3.6) | 11.8 (5.0) | 15.5 (3.6) | 11.7 (3.2) |
| Refinement | SHELX | SHELX | REFMAC | REFMAC |
| Reflections used | 276,976 | 264,777 | 69,514 | 272,435 |
| No. of protein atoms | 3,575 | 3,575 | 3,575 | 7,360 |
| No. of water molecules | 935 | 484 | 396 | 1661 |
| Rfactor | 0.115 | 0.113 | .162 | .150 |
| Rfree | 0.126 | 0.130 | .185 | .172 |
| r.m.s. deviation bond lengths | 0.017 Å | 0.016 Å | .018 Å | 0.007 Å |
| r.m.s. deviation bond angles | 2.048° | 2.086° | 1.714° | 1.244° |
| Average B-factors (Å2) | ||||
| All atoms | 8.9 | 8.3 | 13.1 | 12.4/13.9 |
| Ligand atoms | 10.4 | 10.2 | 9.8 | |
| Ramachandran outliers | 0.5% | 0.5% | 0.5 | 0.5 |
| Ramachandran favored | 96.9% | 96.9% | 96.4 | 96.4 |
| PDB code | 2vk5 | 2bf6 | 2vk6 | 2vk7 |