Table 1.
Data collection and refinement statistics
| Data collection | |
| Beam line | Photon Factory BL5A |
| Wavelength (Å) | 0.97848 |
| Space group | I432 |
| Cell parameters | a = b = c = 272.8 Å |
| Resolution (Å) | 50.0–3.10 (3.21–3.10)a |
| Unique reflections | 31 714 (3126)a |
| Completeness (%) | 99.9 (100.0)a |
| Redundancy | 15.0 (14.6)a |
| Rsymb | 0.094 (0.847)a |
| I/σ(I) | 28.4 (3.49)a |
| Structure refinement | |
| Working-set reflections | 29 484 |
| Test-set reflections | 1556 |
| Resolution (Å) | 50.0–3.10 |
| Number of SerRS subunits | 1 (one half of dimer) |
| Number of RNA molecules | 1 |
| Number of protein atoms | 4363 |
| Number of RNA atoms | 2090 |
| Number of ligands | 1 (Ser-SA) |
| Number of ions | 1 (Zn2+), 8 (sulfate), 15 (Pt2+) |
| Number of solvent molecules | 0 |
| Rwork/Rfreec | 0.204/0.260 |
| Average B factor (Å2) | |
| Overall | 128.4 |
| Protein | 112.0 |
| RNA | 163.0 |
| Ligand | 71.4 |
| Ion | 152.2 |
| RMSD bond lengths (Å) | 0.009 |
| RMSD bond angles (°) | 1.25 |
| Ramachandran-plot analysisd | |
| Most favored regions (%) | 95.2 |
| Additional allowed regions (%) | 4.8 |
| Generously allowed regions (%) | 0.0 |
| Disallowed regions (%) | 0.0 |
aThe statistics in the highest-resolution shell are given in parentheses.
bRsym = ∑hkl∑i[|Ii(hkl) − <I(hkl) > |]/∑hkl∑i[Ii(hkl)], where Ii(hkl) is the intensity of the ith measurement of hkl and <I(hkl)> is the average value of Ii(hkl) for all ith measurements.
cRwork, free = ∑hkl(||Fobs|−k|Fcalc||)/∑hkl(|Fobs|), where Rwork and Rfree are calculated using the working-set and test-set reflections (5% of the total reflections), respectively.
dProcheck (20) was used for Ramachandran-plot analysis.