TABLE 1.
X-ray data collection and structure refinements statics
| Crystal | D50A-Inu | E230A-Fnys |
|---|---|---|
| Data collection | ||
| Unit cell dimensions (Å) | 67.1, 108.6, 96.1 (β = 91.4°) | 65.21, 92.66, 117.75 89.91, 82.96, 85.82 |
| Space group | P21 | P1 |
| Molecules in asymmetric unit | 2 | 4 |
| Solvent content (%) | 42 | 42 |
| Limiting resolution (Å) (outer shell) | 2.24 (2.36–2.24) | 2.68 (2.82–2.68) |
| Unique reflections | 65,603 | 74,146 |
| Rrima | 0.14 (0.51) | 0.22 (0.44) |
| Rpimb | 0.07 (0.24) | 0.11 (0.44) |
| Completeness (%) | 98.4 (98.2) | 96.4 (88.4) |
| Mean multiplicity | 5.2 (5.0) | 4.3 (2.0) |
| Mean I/σI | 5.3 (1.5) | 8.3 (2.9) |
| Final refinement parameters | ||
| Protein atoms (non-H) | 8,100 | 16,200 |
| Solvent molecules | 623 | 279 |
| Ligand molecules | 2 Fru6 | 4 Fructosylnystose |
| Glycosylation molecules | 8 N-acetylglucosamine | 20 N-acetylglucosamine |
| R-factorc | 0.19 | 0.23 |
| Rfree | 0.23 | 0.31 |
| r.m.s.d bonds (Å)/angles (°) | 0.012/1.8 | 0.014/1.8 |
| Averaged B-factors (Å2) | ||
| Main chain | 15.6 | 32.8 |
| Side chain | 16.5 | 33.1 |
| Ligand | 31.2 | 30.0 |
| Solvent | 23.2 | 45.6 |
| Ramachandran plot | ||
| Favored (%) | 98.8 | 96.7 |
| Outliers (%) | 1.2 | 3.3 |
| Protein Data Bank code | 3U14 | 3U75 |
a Rrim = Σ[N/(N − 1)]1/2Σ|I(h)I − 〈I(h)〉|]/ΣΣ〈I(h)〉.
b Rpim = Σ[1/(N − 1)]1/2Σ|I(h)i − 〈I(h)〉|/ΣΣ〈I(h)〉.
c R-factor = Σ(|Fobs − Fcalc|)/Σ|Fobs| (Rfree is equivalent to R-factor for a randomly selected 5% subset of reflections not used in structure refinement).
d r.m.s., root mean square.