Table 1.
Crystallographic data and refinement statistics
| Native Mg·ATP | Native SUMO Mg·ATP | Native/ATP | Hg/ATP | |
|---|---|---|---|---|
| PDB ID | 1Y8Q | 1Y8R | ||
| Source | APS 31ID | APS 31ID | X4A | X4A |
| Wavelength (Å) | 0.9790 | 0.9790 | 1.008 | 1.008 |
| Resolution limits (Å) | 20–2.2 | 20–2.75 | 20–2.5 | 20–2.8 |
| Space group | P21 | P212121 | P21 | P21 |
| Unit cell (Å) a, b, c, α, β, γ | 101.2, 116.7, 106.1, 90, 112.7, 90 | 117.1, 214.1, 100.7, 90, 90, 90 | 101.2, 116.7, 106.0, 90, 112.6, 90 | 101.8, 116.6, 105.6, 90, 112.6, 90 |
| Number of observations | 351 595 | 727 056 | 310 888 | 236 755 |
| Number of reflections | 108 617 | 67 058 | 74 210 | 104 523a |
| Completeness (%) | 97.3 (92.7) | 93.4 (75.9) | 98.5 (97.0) | 96.3 (92.8) |
| Mean I/σI | 16.4 (2.6) | 9.7 (3.0) | 6.2 (1.5) | 4.3 (1.0) |
| Rmerge on Ib | 7.1 (43.5) | 15.0 (48.4) | 13.2 (57.7) | 17.8 (84.1) |
| Cutoff criteria I/σI | −0.5 | −0.7 | −0.5 | −1.0 |
| Number of sites | 12 | |||
| MFID (%)c | 18.6 | |||
| Mean FOM (SOLVE)d | 0.15 (acentric)/0.21 (centric) | |||
| FOM (RESOLVE with NCS) | 0.50 (acentric)/0.61 (centric) | |||
| Refinement statistics | ||||
| Resolution limits (Å) | 20–2.25 | 20–2.75 | ||
| Number of reflections | 104 390 | 63 543 | ||
| Completeness (%) | 97.0 (93.2) | 94.9 (84.3) | ||
| Cutoff criteria I/σI | 0 | 0 | ||
| Protein/ligand/water atoms | 12 935/66/820 | 14 316/66/317 | ||
| Rcryste | 0.208 (0.350) | 0.220 (0.370) | ||
| Rfree (5% of data) | 0.248 (0.371) | 0.276 (0.391) | ||
| Bonds (Å)f | 0.006 | 0.009 | ||
| Angles (deg)f | 1.1 | 1.2 | ||
| B-factors (mc/sc in Å2)f | 1.50/2.14 | 1.4/1.8 | ||
| aSIRAS data completeness treats Bijvoët mates independently. | ||||
| bRmerge=∑hkl∑i∣I(hkl)i−〈I(hkl)〉∣/∑hkl∑i〈I(hkl)i〉. | ||||
| cMFID (mean fractional isomorphous difference)=∑∣∣Fph∣−∣Fp∣∣/∑∣Fp∣, where Fp is the protein structure factor amplitude and ∣Fph∣ is the heavy-atom derivative structure factor amplitude. | ||||
| dMean FOM=combined figure of merit. | ||||
| eRcryst=∑hkl∣Fo(hkl)−Fc(hkl)∣ /∑hkl∣Fo(hkl)∣, where Fo and Fc are the observed and calculated structure factors, respectively. | ||||
| fValues indicate root-mean-square deviations in bond lengths, bond angles, and B-factors of bonded atoms. | ||||
| Values in parentheses indicate statistics for the high-resolution data bin. | ||||