TABLE 1.
X-ray diffraction data collection and refinement
Values for the outer resolution shell of data are given in parentheses. APS, Advanced Photon Source; ALS, Advanced Light Source.
| Se-Met | Sulfate complex | AfUGMr | AfUGMr-UDP | AfUGMr-UDP-Galp | |
|---|---|---|---|---|---|
| Beamline | APS 19ID | APS 19ID | ALS 8.2.2 | ALS 8.2.2 | APS 24-ID-C |
| Active site ligand | Sulfate | Sulfate | None | UDP | UDP-Galp |
| Space group | P6522 | P6522 | P6522 | P6522 | P6522 |
| Unit cell parameters (Å) | a = 218.1, c = 319.1 | a = 217.8, c = 319.7 | a = 217.9, c = 322.8 | a = 218.2, c = 320.8 | a = 219.1, c = 322.4 |
| Wavelength | 0.97915 | 0.97915 | 1.00000 | 1.00000 | 0.97949 |
| Resolution (Å) | 55.00-2.65 (2.74-2.65) | 50.0-2.35 (2.43-2.35) | 48.6-2.25 (2.37-2.25) | 48.6-2.25 (2.37-2.25) | 48.8-2.25 (2.37-2.25) |
| Observations | 1,833,668 | 900,659 | 1,560,709 | 1,036,765 | 1,670,151 |
| Unique reflections | 128,441 | 167,455 | 211,192 | 205,755 | 207,614 |
| Rmerge (I) | 0.087 (0.351) | 0.086 (0.568) | 0.097 (0.599) | 0.086 (0.676) | 0.097 (0.599) |
| Rmeas (I) | 0.104 (0.643) | 0.096 (0.753) | 0.104 (0.645) | ||
| Rpim (I) | 0.038 (0.231) | 0.041 (0.323) | 0.035 (0.232) | ||
| Mean I/σ | 32.3 (5.5) | 20.1 (3.0) | 16.2 (3.5) | 17.6 (2.8) | 13.9 (3.4) |
| Completeness (%) | 99.0 (99.6) | 90.5 (91.1) | 99.8 (100.0) | 97.9 (99.7) | 97.3 (97.6) |
| Multiplicity | 14.3 (12.7) | 5.4 (5.4) | 7.4 (7.4) | 5.0 (5.0) | 8.0 (7.0) |
| No. of protein chains | 4 | 4 | 4 | 4 | |
| No. of protein residues | 2018 | 2020 | 2019 | 2019 | |
| No. of protein atoms | 15,597 | 15,580 | 15,551 | 15,562 | |
| No. of FAD atoms | 212 | 212 | 212 | 212 | |
| No. of ligand atoms | 0 | 0 | 50 | 72 | |
| No. of water molecules | 516 | 813 | 657 | 659 | |
| Rcryst | 0.188 (0.249) | 0.190 (0.244) | 0.192 (0.260) | 0.185 (0.249) | |
| Rfreea | 0.218 (0.297) | 0.215 (0.281) | 0.218 (0.297) | 0.210 (0.294) | |
| r.m.s.d.b bond lengths, Åc | 0.007 | 0.007 | 0.007 | 0.007 | |
| r.m.s.d.b bond angles, ° | 1.06 | 1.04 | 1.07 | 1.08 | |
| Ramachandran plotd | |||||
| Favored (no. of residues) | 1985 | 1983 | 1979 | 1977 | |
| Allowed (no. of residues) | 25 | 29 | 32 | 34 | |
| Outliers (no. of residues) | 0 | 0 | 0 | 0 | |
| Average B-factor (Å2) | |||||
| Protein | 35 | 30 | 33 | 35 | |
| FAD | 32 | 25 | 30 | 31 | |
| Active site ligand | 56 | 26 | 39 | ||
| Water | 34 | 34 | 34 | 37 | |
| Coordinate error (Å)e | 0.33 | 0.32 | 0.32 | 0.32 | |
| PDB code | 3UTE | 3UTF | 3UTG | 3UTH |