TABLE 1.
Data collection and refinement statistics. Values in parentheses refer to the highest resolution shell
| Crystal | a | b | c | d | e | f | g | h | i |
|---|---|---|---|---|---|---|---|---|---|
| Protein Data Bank code | 4YZ1 | 4YW2 | 4YZ5 | 4YW1 | 4YZ2 | 4YW3 | 4YZ4 | 4YW0 | 4YW5 |
| CBM complex | 6′SL | 3′SL | Neu5Ac | Neu5Ac | Neu5Ac | 2,3F-Neu5Ac | |||
| Active site complex | Neu5Ac2en | Neu5Ac2en | Neu5Ac2en | Neu5Ac2en | 3F-β-Neu5Ac | OC | |||
| Soaking conditions | |||||||||
| Compound | None | 6′SL | 3′SL | 3′SL | Neu5Ac2en | Neu5Ac2en | Neu5Ac | 2,3F-Neu5Ac | OC |
| Concentration (mm) | 20 | 200 | 20 | 50 | 20 | 200 | 5 | 20 | |
| Time (min) | 45 | 2 | 15 | 2 | 45 | 2 | 45 | 5 | |
| Data Collection | |||||||||
| X-ray source | DLS I04 | Rigaku 007HFM | DLS I04 | Rigaku 007HFM | DLS I04 | Rigaku 007HFM | DLS I04 | Rigaku 007HFM | Rigaku 007HFM |
| Space group and cell dimensions (Å,°) | P212121 | P1211 | P212121 | P1211 | P212121 | P1211 | P212121 | P1211 | P1211 |
| a = 150.13, b = 73.74, c = 136.13 | a = 100.65, b = 74.91, c = 113.00, β = 96.21 | a = 73.47, b = 136.57, c = 150.07 | a = 100.83, b = 74.95, c = 113.30, β = 96.35 | a = 73.30, b = 136.71, c = 150.79 | a = 100.62, b = 74.73, c = 113.01, β = 96.35 | a = 73.38, b = 136.09, c = 150.44, | a = 100.24, b = 74.84, c = 113.35, β = 96.31 | a = 99.55, b = 74.05, c = 112.12, β = 95.50 | |
| Resolution (Å) | 101.05–1.97 (2.2–1.97) | 30.00–2.00 (2.05–2.00) | 75.04–2.27 (2.33–2.27) | 40.00–2.25 (2.31–2.25) | 101.28–2.06 (2.11–2.06) | 30.00–2.05 (2.10–2.05) | 100.92–2.05 (2.21–2.15) | 30.00–2.05 (2.10–2.05) | 40.00–2.30 (2.34–2.30) |
| Unique reflections | 107,569 | 109,231 | 70,273 | 75,606 | 93,784 | 97,981 | 81,664 | 102,205 | 71,545 |
| Completeness (%) | 98.52 (98.14) | 96.43 (92.05) | 99.46 (99.42) | 94.15 (95.58) | 99.34 (99.33) | 93.27 (56.66) | 98.77 (97.28) | 97.73 (76.33) | 99.8 (98.8) |
| Redundancy | 3.1 (3.0) | 3.7 (3.6) | 4.5 (4.6) | 2.6 (2.5) | 4 (4) | 3.4 (2.2) | 5.4 (5.5) | 3.5 (2.8) | 3.1 (2.8) |
| Rmerge | 0.099 (0.533) | 0.109 (0.476) | 0.326 (1.375) | 0.121 (0.482) | 0.137 (0.509) | 0.096 (0.404) | 0.140 (0.636) | 0.107 (0.576) | 0.089 (0.724) |
| I/σI | 13.9 (1.93) | 18.39 (3.88) | 6.0 (2.5) | 11.64 (2.49) | 7.1 (2.3) | 17.67 (3.02) | 7.6 (2.7) | 15.97 (2.49) | 14.78 (1.93) |
| Refinement | |||||||||
| Reflections used | 100,672 | 103,624 | 66,621 | 71,657 | 89,017 | 93,033 | 77,515 | 96,897 | 67,786 |
| No. of protein atoms | 10,433 | 10,460 | 10,503 | 10,444 | 10,465 | 10,463 | 10,466 | 10,460 | 10,452 |
| No. of ligand atoms | 60 | 105 | 50 | 84 | 50 | 85 | 60 | 92 | 98 |
| No. of water | 818 | 870 | 721 | 857 | 907 | 728 | 640 | 557 | 344 |
| R factor | 0.181 | 0.180 | 0.218 | 0.209 | 0.207 | 0.172 | 0.203 | 0.197 | 0.207 |
| Rfree | 0.215 | 0.209 | 0.269 | 0.249 | 0.243 | 0.203 | 0.239 | 0.233 | 0.239 |
| Root mean square deviation bond lengths (Å) | 0.015 | 0.012 | 0.010 | 0.009 | 0.017 | 0.013 | 0.013 | 0.016 | 0.010 |
| Root mean square deviation bond angles (°) | 1.643 | 1.499 | 1.466 | 1.396 | 1.727 | 1.553 | 1.537 | 1.645 | 1.160 |
| Ramachandran (favored/outlier) | 97.02/0.00 | 97.09/0.00 | 96.63/0.00 | 97.03/0.23 | 96.64/0.00 | 96.73/0.08 | 96.94/0.08 | 97.19/0.08 | 97.26/0.15 |
| Average B-factors (Å2) | |||||||||
| All atoms | 31.3 | 25.9 | 21.5 | 33.0 | 15.9 | 25.3 | 26.6 | 31.6 | 40.9 |
| Protein atoms | 31.0 | 22.7 | 21.2 | 33.0 | 15.3 | 25.2 | 26.3 | 31.7 | 47.5 |
| Ligand/ion atoms | 58.8 | 35.9 | 46.5 | 32.1 | 39.6 | 26.7 | 57.0 | 29.9 | 40.6 |
| Waters | 32.5 | 26.9 | 20.7 | 33.8 | 19.8 | 27.2 | 28.0 | 28.8 | 37.5 |