TABLE 1.
Refinement statistics
| Parameter | Value for the protein or complex |
||||
|---|---|---|---|---|---|
| 3D(K18E) | 3D(K18E)-RNA | 3D(K20E) | 3D(K20E)-RNA | 3D(K20A)-RNA | |
| Data collection | |||||
| Beamline | SLSb | ID14.4 (ESRF) | PX1 (Soleil)c | ID14.4 (ESRF) | XALOC (Alba) |
| Resolution (Å) | 30.0–2.00 | 30–2.57 | 46.6–1.8 | 30–2.8 | 47.11–2.94 |
| Space group | P41212 | P3221 | P41212 | P3221 | P41212 |
| Cell dimensions | |||||
| a, b, c (Å) | 91.6, 91.6, 117.8 | 94.6, 94.6, 101.0 | 91.7, 91.7, 118.1 | 95.2, 95.2, 101.3 | 94.2, 94.2, 121.5 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 120 | 90, 90, 90 | 90, 90, 120 | 90, 90, 90 |
| Rmerge | 6.1 | 6.5 | 5.9 | 10.6 | 9.8 |
| I/sI | 25.6 | 9.3 | 24.15 | 10.7 | 12.8 |
| Completeness (%) | 99.9 | 99.0 | 99.8 | 100 | 99.6 |
| Multiplicity | 6.5 | 2.8 | 8.7 | 5.4 | 6.7 |
| Refinement | |||||
| Resolution (Å) | 30.0–2.00 | 30.0–2.57 | 46.6–1.8 | 30–2.8 | 47.11–2.94 |
| No. of reflections | |||||
| Total | 225,734 | 89,958 | 412,193 | 72,396 | 82,046 |
| Unique | 34,625 | 19,374 | 47,356 | 13,477 | 12,228 |
| Rwork/Rfreea | 21.47/24.76 | 23.33/25.67 | 20.29/22.66 | 24.61/26.60 | 20.79/25.82 |
| No. of residues | |||||
| Protein | 476 | 473 | 477 | 473 | 475 |
| RNA | 15 | 15 | 13 | ||
| Water | 147 | 31 | 280 | 12 | 14 |
| Ligands (no.) | 5 | 3 | 6 | 1 | 1 |
| B factors (Å2) | 17.34 | 38.761 | 26.58 | 46.92 | 52.64 |
| Protein | 17.22 | 33.642 | 25.90 | 42.48 | 49.22 |
| RNA | 95.400 | 99.25 | 98.45 | ||
| Water + ligands + ions | 19.99 | 54.824 | 34.64 | 58.95 | 53.65 |
| RMSD | |||||
| Bond lengths (Å) | 0.004 | 0.004 | 0.004 | 0.004 | 0.004 |
| Bond angles (°) | 0.810 | 0.738 | 0.791 | 0.723 | 0.763 |
| Ramachandran plot (% [no. of residues in the region/total no. of residues) | |||||
| Preferred regions | 98.7 (470/476) | 97 (459/473) | 99.2 (473/477) | 97 (459/473) | 98.1 (467/475) |
| Allowed regions | 1.3 (6/476) | 3 (14/473) | 0.8 (4/477) | 3 (14/473) | 1.7 (8/475) |
a
Rwork = ∑hkl ||Fobs(hkl)| − |Fcalc(hkl)||/∑hkl | Fobs(hkl)|, where Fobs and Fcalc are the structure factors, deduced from measured intensities and calculated from the model, respectively. Rfree is equivalent to Rwork but for 5% of the total reflections chosen at random and omitted from refinement. hkl, Miller index.
b
Swiss Light Source, Paul Scherrer Institut, Switzerland.
c
Soleil Synchrotron, Gif sur Yvette, France.