Table 3.
X-ray data collection and structure statistics for RafE
The values for highest resolution shells are shown in parentheses. CIT, citric acid; EDO, ethylene glycol.
| RafE |
|||
|---|---|---|---|
| Raffinose | Stachyose | Verbascose | |
| Data collection | |||
| Beamline | Home Beam | Home Beam | Home Beam |
| Wavelength (Å) | 1.540 | 1.540 | 1.540 |
| Space group | P21 | P212121 | P21 |
| Cell dimensions (a, b, c) (Å) | 48.86, 145.82, 118.68 | 49.28, 118.84, 146.01 | 48.92, 145.88, 118.37 |
| Resolution (Å) | 30.00–2.65 (2.70–2.65) | 30.00–2.35 (2.39–2.35) | 30.00–2.40 (2.44–2.40) |
| Rmerge | 0.142 (0.565) | 0.084 (0.181) | 0.152 (0.530) |
| Rpim | 0.083 (0.369) | 0.036 (0.095) | 0.076 (0.344) |
| CC½ | 0.987 (0.729) | 0.995 (0.966) | 0.984 (0.706) |
| <I/σI> | 11.0 (2.0) | 20.2 (6.7) | 9.4 (2.2) |
| Completeness (%) | 99.9 (100.0) | 99.9 (99.8) | 99.6 (94.3) |
| Redundancy | 4.0 (3.6) | 5.0 (3.6) | 4.0 (3.1) |
| No. of reflections | 191,428 | 183,357 | 255,814 |
| No. unique | 47,919 | 36,605 | 64,353 |
| Refinement | |||
| Resolution (Å) | 2.65 | 2.35 | 2.40 |
| Rwork/Rfree | 0.24/0.29 | 0.22/0.24 | 0.23/0.26 |
| No. of atoms | |||
| Protein | 2968 (A), 2967 (B), 2972 (C), 2882 (D) | 3001 (A), 2986 (B) | 2991 (A), 2979 (B), 3000 (C), 2934 (D) |
| Ligand | 34 (RAFFINOSE-A), 34 (RAFFINOSE-B), 34 (RAFFINOSE-C), 34 (RAFFINOSE-D) | 45 (STACHYOSE-A), 45 (STACHYOSE-B), 26 (CIT), 16 (EDO) | 56 (VERBASCOSE-A), 56 (VERBASCOSE-B), 56 (VERBASCOSE-C), 56 (VERBASCOSE-D), 4 (EDO) |
| Water | 239 | 363 | 304 |
| B-factors | |||
| Protein | 36.4 (A), 40.0 (B), 39.3 (C), 49.0 (D) | 28.0 (A), 30.0 (B) | 32.8 (A), 36.6 (B), 34.9 (C), 47.5 (D) |
| Ligand | 31.3 (RAFFINOSE-A), 33.7 (RAFFINOSE-B), 37.3 (RAFFINOSE-C), 37.5 (RAFFINOSE-D) | 25.0 (STACHYOSE-A), 29.9 (STACHYOSE-B), 48.7 (CIT), 49.8 (EDO) | 33.4 (VERBASCOSE-A), 36.6 (VERBASCOSE-B), 34.6 (VERBASCOSE-C), 41.8 (VERBASCOSE-D), 32.1 (EDO) |
| Water | 31.3 | 32.2 | 31.4 |
| Root-mean-square deviation | |||
| Bond lengths (Å) | 0.006 | 0.006 | 0.006 |
| Bond angles (°) | 1.07 | 1.11 | 1.06 |
| Ramachandran (%) | |||
| Preferred | 96.9 | 97.8 | 96.7 |
| Allowed | 3.1 | 2.2 | 3.3 |
| Outliers | 0.0 | 0.0 | 0.0 |