Table 1.
Summary of data collection and refinement statistics for Ega3
Values in parentheses correspond to the highest resolution shell.
| Ega3 | Ega3-GalN | |
|---|---|---|
| Data collection | ||
| Beamline | CLS 08BM-1 | NSLS II 17ID-1 |
| Wavelength (Å) | 0.9792 | 0.9996 |
| Space group | P212121 | P212121 |
| Unit-cell parameters (Å,°) | a = 44.6, b = 47.3, c = 152.5; α = β = γ = 90.0 | a = 44.8, b = 48.1, c = 163.4; α = β = γ = 90.0 |
| Resolution (Å) | 42.8–1.76 (1.82–1.76) | 30.00–2.09 (2.17–2.09) |
| Total no. of reflections | 457,277 | 156,678 |
| No. of unique reflections | 32,553 | 21,680 |
| Redundancy | 14.0 (11.4) | 7.2 (7.0) |
| Completeness (%) | 99.8 (88.7) | 99.7 (98.6) |
| Average I/σ(I) | 28.1 (4.27) | 11.25 (2.24) |
| Rmerge (%)a | 6.3 (59.4) | 12.4 (81.2) |
| CC½ (%)b | 100 (91.7) | 99.9 (95.6) |
| Refinement | ||
| Rworkc/Rfreed | 16.4/19.4 | 16.7/21.0 |
| CCwork/CCfree | 96.6/96.0 | 96.7/94.6 |
| No. of atoms | ||
| Protein | 1956 | 1958 |
| Glycan | 208 | 245 |
| GalN | 12 | |
| Water | 241 | 185 |
| Average B-factors (Å2)e | 31.3 | 36.2 |
| Protein | 27.4 | 32.3 |
| Glycan | 59.6 | 63.2 |
| GalN | 30.7 | |
| Water | 38.3 | 42.2 |
| RMSD | ||
| Bond lengths (Å) | 0.008 | 0.008 |
| Bond angles (°) | 1.032 | 1.038 |
| Ramachandran plote | ||
| Total favored (%) | 99 | 99 |
| Total allowed (%) | 100 | 100 |
| Coordinate error (Å)f | 0.13 | 0.11 |
| PDB code | 6OJ1 | 6OJB |
aRmerge = ∑hkl∑j|Ihkl(j) − 〈Ihkl〉|/∑hkl∑j Ihkl(j), where Ihkl(j) and 〈Ihkl〉 represent the diffraction intensity values of the individual measurements, and the corresponding mean values, for each unique reflection. The summation is over all unique measurements.
b CC½ is the ratio of Pearson correlation coefficients (CC = ∑(x − 〈x〉) (ml − 〈ml〉)/(∑(x − 〈x〉)2∑(ml − 〈ml〉)2)1/2) between random half-sets of data.
c Rwork = ∑‖Fobs| − k|Fcalc‖/|Fobs|,where Fobs and Fcalc are the observed and calculated structure factors, respectively.
d Rfree is the sum extended over a subset of reflections (4.89% apo and 9.27% GalN-bound) excluded from all stages of the refinement.
e Data are as calculated using MolProbity (89).
f Maximum-likelihood-based coordinate error, as determined by PHENIX (81).