Table 2. Refinement statistics.
| Crystal | Xyl | Xyl•arabinose | Xyl•xylose | Xyl•arabinose• xylose |
|---|---|---|---|---|
| Resolution range (Å) | 46.13–1.70 | 45.48–2.10 | 46.35–1.90 | 41.85–1.70 |
| Number of reflections | 56950 | 29435 | 40994 | 54015 |
| R-factor (%)† | 14.82 | 14.93 | 21.61 | 15.91 |
| Rfree (%)‡ | 17.59 | 19.95 | 25.90 | 19.04 |
| Number of atoms: | ||||
| - Totals | 4654 | 4535 | 4595 | 4610 |
| - Protein | 4053 | 4053 | 4053 | 4053 |
| - Ca2+ ion | 1 | 1 | 1 | 1 |
| - Water molecules | 570 | 471 | 531 | 516 |
| - Glycerol | 30 | - | - | - |
| - L-Arabinose | - | 10 | - | 10 |
| - D-Xylose | - | - | 10 | 30 |
| RMSDs: | ||||
| - Bond lengths (Å) | 0.012 | 0.012 | 0.011 | 0.011 |
| - Bond angles (deg) | 1.55 | 1.54 | 1.45 | 1.44 |
| - Chiral volume (Å3) | 0.10 | 0.10 | 0.10 | 0.10 |
| Ramachandran statistics:§ | ||||
| - In preferred regions (%) | 96.35 | 96.00 | 96.59 | 95.94 |
| - In allowed regions (%) | 3.04 | 2.80 | 2.21 | 3.25 |
| - In disallowed regions (%) | 0.61 | 1.20 | 1.20 | 0.81 |
| Mean B values (Å2): | ||||
| - Overall | 17.3 | 19.6 | 19.9 | 16.8 |
| - Protein | 15.6 | 18.7 | 18.6 | 15.3 |
| - Ca2+ ion | 15.3 | 25.2 | 18.1 | 13.3 |
| - Water molecules | 29.1 | 27.6 | 30.0 | 28.0 |
| - Glycerol | 27.5 | - | - | - |
| - L-Arabinose | - | 11.9 | - | 8.7 |
| - D-Xylose | - | - | 25.4 | 22.1¶ |
| PDB code | 5Z5D | 5Z5F | 5Z5H | 5Z5I |
† R-factor = ∑hkl ||FP(obs)| − |FP(calc)||/∑hkl|FP(obs)|, where |FP(obs)| and |FP(calc)| are observed and calculated structure factor amplitudes, respectively.
‡ Rfree is R-factor for 5% of the data not included in the refinement selected in thin shells.
§ Ramachandran statistics were obtained from the program COOT [28].
¶ B value of D-xylose in subsite +1 (see text). Mean B value for all three D-xylose molecules is 37.7 Å2.