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. 2020 Jun 29;295(34):11949–11962. doi: 10.1074/jbc.RA120.014555

Table 2.

Data collection and refinement statistics

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)
    II 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).