TABLE 1.
Data collection and processing
Figures in parentheses refer to the highest resolution bin.
| Data collection | Native | ManNAc bound |
| Synchrotron station | SRS 14.1 | DLS I04 |
| Wavelength (Å) | 1.488 | 0.9745 |
| Space group | P4 | P4 |
| Cell dimensions | a = b = 118.56 Å, c = 44.25 Å | a = b = 119.54 Å, c = 44.26 Å |
| Resolution range (Å) | 41.9–2.0 (2.11–2.00) | 53.5–2.1 (2.21–2.10) |
| Observations | 130,094 (16,153) | 156,110 (23,101) |
| Unique reflections | 41,125 (5,672) | 36,910 (5,361) |
| Completeness (%) | 97.8 (93.3) | 99.8 (100.0) |
| Rmergea | 0.066 (0.214) | 0.069 (0.174) |
| I/σ(I) | 8.0 (2.9) | 6.1 (4.2) |
| Refinement | ||
| Protein atoms | 3,520 | 3,531 |
| Residues chain A | 239–457 | 239–458 |
| Residues chain B | 239–457 | 239–457 |
| Water molecules | 297 | 321 |
| Other molecules | ||
| Subunit | A B | A B |
| Calcium ions | 1 1 | 1 1 |
| Sulfate ions | 2 1 | 1 1 |
| Acetate ions | 1 | |
| GlcNAc | 1 | 1 |
| Glycerol | 1 | |
| ManNAc ligand | 1 1 | |
| Rworkb (%) | 18.3 | 18.7 |
| Rfreec (%) | 20.9 | 21.4 |
| r.m.s.d.d bond length (Å) | 0.005 | 0.006 |
| r.m.s.d. bond angle (°) | 1.32 | 1.30 |
| Average B-values (Å2) | ||
| Protein | 20.2 | 16.9 |
| Water | 32.4 | 28.8 |
| Other hetero-atoms | 40.7 | 34.1 |
| PDB ID | 4M7H | 4M7F |
| Ramachandran plot valuese (%) | ||
| Favored | 93.3 | 93.5 |
| Allowed | 6.7 | 6.5 |
| Outliers | 0.0 | 0.0 |
a Rmerge = ΣhΣj|Ih,j − Ih|/ΣhΣj|Ih,j|, where Ih,j is the jth observation of reflection h and Ih is the mean of the j measurements of reflection h.
b Rwork = Σh‖Foh| − |Fch‖ /Σh |Foh| where Foh and Fch are the observed and calculated structure factor amplitudes, respectively, for the reflection h.
c Rfree is equivalent to Rwork for a randomly selected subset (5%) of reflections not used in the refinement.
d r.m.s.d., root mean square deviation.
e Defined according to Molprobity.