TABLE 1.
Data collection and refinement statistics
Numbers in parentheses refer to the appropriate outer resolution shell. SeMet, selenomethonine; r.m.s.d., root mean square deviation from ideal geometry.
| Parameters | a | b | c | d |
|---|---|---|---|---|
| SeMet-NST·CMP complex | SeMet-NST Free enzyme | NST·CDP complex | NST·CMP-3F(axial)-Neu5Ac complex | |
| Ligand(s) used for co-crystallization | CMP-3F(equatorial)-Neu5Ac + Lactose | CDP | CMP-3F(axial)-Neu5Ac + n-propyl lactoside | |
| Ligand observed in the structure | CMP | CDP | CMP-3F(axial)-Neu5Ac | |
| Lipid binding site modeled witha | PEG | Triton X-100 | PEG | PEG |
| PDB entry | 2yk5 | 2yk4 | 2yk6 | 2yk7 |
| Data collection statistics | ||||
| Beamline | ALS 822 | ALS 822 | Rigaku MicroMax 007HF | Rigaku MicroMax 007HF |
| Wavelength (Å) | 0.980 | 0.980 | 1.54 | 1.54 |
| Resolution limits (Å) | 2.33 (2.41-2.33) | 1.94 (1.97-1.94) | 2.83 (2.88-2.83) | 2.18 (2.22-2.18) |
| Space group | P21212 | P21212 | P21212 | C2221 |
| Unit cell dimension (Å) | 85.7, 124.1, 41.9 | 86.6, 124.7, 41.9 | 86.1, 123.5, 41.7 | 42.8, 101.4, 166.6 |
| Unique reflections | 19,839 | 34,365 | 11,162 | 19,377 |
| Redundancy | 7.1 (7.1) | 8.8 (8.5) | 6.8 (5.1) | 7.6 (5.4) |
| Completeness (%) | 100.0 (100.0) | 100 (99.9) | 99.7 (97.8) | 97.1 (84.9) |
| I/σ(I) | 17.0 (3.89) | 35.5 (3.22) | 15.4 (2.70) | 23.9 (2.64) |
| Rmerge (%) | 13.7 (40.0) | 6.7 (46.2) | 12.1 (52.2) | 9.0 (46.7) |
| Mosaicity | 0.18-0.26 | 0.20-0.32 | 0.38-0.47 | 0.68-0.82 |
| Refinement statistics | ||||
| Resolution limits (Å) | 2.3 | 2.0 | 2.8 | 2.2 |
| Number of reflections in working set | 18,825 | 32,604 | 10,613 | 17,844 |
| Number of reflections in test set | 1,008 | 1,735 | 529 | 957 |
| Rfactor of working set (%) | 17.5 | 19.3 | 18.1 | 19.6 |
| Rfree (%) | 22.0 | 22.0 | 24.0 | 25.3 |
| r.m.s.d. bond length (Å) | 0.019 | 0.020 | 0.020 | 0.019 |
| r.m.s.d. bond angles (°) | 1.680 | 1.880 | 1.835 | 1.773 |
| Average B factors (Å2) | 20.7 | 33.0 | 28.4 | 30.4 |
| Ramachandran analysis (most favored, allowed, disallowed) | 98.2, 1.8, 0% | 99.4, 0.6, 0% | 95.0, 5.0, 0% | 97.8, 2.2, 0% |
a The head group of the detergent Triton X-100 is polyethylene glycol (PEG) composed of 9 or 10 units of ethylene glycol.