Table 1.
Data Collection and Refinement Statistics
| ΨMP glycosidase | ΨMP glycosidase / ring-opened R5P | glycosidase/ring-opened ribose ΨMP | K166A/ΨMP | |
|---|---|---|---|---|
| beamline | APS 24-ID-C | APS 24-ID-C | APS 24-ID-C | CHESS F1 |
| wavelength (Å) | 0.9792 | 0.9795 | 0.9795 | 0.9180 |
| space group | P212121 | P212121 | P212121 | P212121 |
| a (Å) | 62.1 | 61.3 | 61.5 | 60.7 |
| b (Å) | 115.4 | 116.5 | 77.1 | 76.4 |
| c (Å) | 132.0 | 132.2 | 200.0 | 199.0 |
| chains per asymmetric unit | 3 | 3 | 3 | 3 |
| resolution (Å) | 43.5-2.0 (1.94-1.96)a | 41.2-2.2 (2.19-2.32) | 48.1-2.5 (2.50-2.57) | 35.3-1.8 (1.80-1.82) |
| total no. of reflections | 404995 | 196780 | 124598 | 422749 |
| number of unique reflections | 70995 | 49316 | 33815 | 86433 |
| redundancy | 5.7 (5.5) | 4.0 (4.0) | 3.7 (3.4) | 4.9 (4.9) |
| Rmerge (%)b | 5.5 (34.3) | 6.0 (40.9) | 7.5 (44.1) | 7.3(43.1) |
| I/σ(I) | 25.1 (4.2) | 17.6 (2.4) | 17.5 (3.1) | 20.4 (3.6) |
| no. of reflections | 66972 | 45946 | 31542 | 81618 |
| in working set completeness (%) | 99.7 (99.6) | 99.8 (99.9) | 99.1 (96.9) | 99.1(100) |
| Rwork/ Rfreec (%) | 18.5/22.0 | 17.9/23.1 | 18.5/26.1 | 17.7/20.7 |
| no. of protein atoms | 6423 | 6533 | 6399 | 6575 |
| no. of ligand atoms | 18 | 69 | 93 | 66 |
| no. of water atoms | 375 | 328 | 210 | 644 |
| average B-factor protein (Å2) | 35.0 | 41.4 | 53.5 | 27.3 |
| average B-factor water (Å2) | 34.1 | 37.3 | 39.9 | 31.3 |
| average B-factor ligand (Å2) | 57.7 | 39.5 | 49.5 | 17.6 |
| rmsd for bonds (Å) | 0.008 | 0.007 | 0.008 | 0.007 |
| rmsd for angles (°) | 1.2 | 1.2 | 1.3 | 1.2 |
a
Values in parentheses are for the highest resolution shell.
b
Rmerge = ΣΣi | Ii – <I> | / Σ <I>, where <I> is the mean intensity of the N reflections with intensities Ii and common indices h,k,l.
c
R = Σhkl| |Fobs| – k |Fcal| | / Σhkl |Fobs| where Fobs and Fcal are observed and calculated structure factors. Rwork = is calculated over all reflections used in the refinement. Rfree is calculated over a subset of reflections (5%) excluded from all stages of refinement.