Table 2.
PelXC232S + UDP-GlcNAca | PelXC232S/Y146F/S121A + UDP-GlcNAc | PelXC232S/Y146F/S121A + UDP-GalNAc | |
---|---|---|---|
Data Collection | |||
Wavelength (Å) | 1.075 | 1.075 | 1.075 |
Space group | P21212 | P21212 | P21212 |
Cell dimensions | |||
a, b, c (Å) | 123.0, 75.5, 79.2 | 124.2, 75.5, 79.3 | 123.6, 75.3, 79.3 |
α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
Resolution (Å) | 50.00 – 2.1 (2.18-2.10) | 50.00 - 2.1 (2.18-2.10) | 50.00 -2.1 (2.18-2.10) |
Total no. of reflections | 676002 | 598870 | 589555 |
Total no. of unique reflections | 43495 | 43637 | 44099 |
Rmerge (%)b | 8.0 (58.0) | 12.2 (72.2) | 10.6 (78.7) |
I/σI | 38.8 (5.3) | 23.6 (3.6) | 26.5 (3.1) |
Completeness (%) | 100.0 (100.0) | 100.0 (100.0) | 99.5 (98.6) |
Redundancy | 11.4 (14.6)c | 7.6 (12.5) | 7.6 (12.2) |
Refinement | |||
Rwork/Rfree (%)d | 16.7/19.7 | 15.6/19.5 | 15.6/19.5 |
Average B-factors (Å2) | |||
Protein | 41.29 | 31.23 | 35.80 |
NAD | 32.25 | 21.64 | 25.42 |
UDP-sugar | 40.82 | 33.13 | 33.19 |
Water | 41.52 | 37.69 | 40.39 |
r.m.s. deviations | |||
Bond lengths (Å) | 0.006 | 0.006 | 0.006 |
Bond angles (°) | 0.881 | 0.863 | 0.897 |
Ramachandran plot (%)e | |||
Total favored | 97.87 | 97.55 | 97.71 |
Total allowed | 2.13 | 2.45 | 2.13 |
Coordinate error (Å)f | 0.21 | 0.2 | 0.22 |
PDB code | 6WJB | 6WJ9 | 6WJA |
a Although this structure was crystallized with UDP-GlcNAc, density for the sugar was not visible and therefore only UDP was modeled and refined.
b Rmerge = Σ Σ |I(k) − |/Σ I(k), where I(k) and represent the diffraction intensity values of the individual measurements and the corresponding mean values. The summation is over all unique measurements.
c Values in parentheses correspond to the highest resolution shell.
d Rwork = Σ ‖Fobs| − k|Fcalc‖/|Fobs|, where Fobs and Fcalc are the observed and calculated structure factors, respectively. Rfree is the sum extended over a subset of reflections (5%) excluded from all stages of the refinement.
e As calculated using MOLPROBITY (54).
f Maximum-Likelihood Based Coordinate Error, as determined by PHENIX (52).