Table S1.
Data collection and refinement statistics
| Data collection and refinement | TrmD-AdoMet | TrmD-sinefungin | TrmD-WT tRNA -sinefungin | TrmD-36U tRNA -sinefungin | TrmD-36C tRNA -sinefungin |
| Data collection | |||||
| Beam line | BL-NW12A in PF | BL5A in PF | BL41XU in SP8 | BL-NE3A in PF | BL32XU in SP8 |
| Space group | R32:H | R32:H | P41212 | P41212 | P41212 |
| Cell dimensions | |||||
| a, b, c (Å) | 93.9, 93.9, 178.0 | 93.8, 93.8, 177.9 | 86.8, 86.8, 227.0 | 87.4, 87.4, 229.0 | 87.5, 87.5, 228.7 |
| α, β, γ (°) | 90, 90, 120 | 90, 90, 120 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å) | 50.00–1.55 (1.58–1.55) | 50.00–1.60 (1.63–1.60) | 50.00–3.00 (3.11–3.00) | 50.00–2.90 (3.00–2.90) | 50.00–3.00 (3.11–3.00) |
| Rsym | 0.064 (0.969) | 0.061 (0.553) | 0.121 (0.875) | 0.151 (0.852) | 0.153 (0.694) |
| I/σI | 43.7 (3.0) | 30.2 (3.6) | 20.7 (2.1) | 20.0 (2.5) | 20.2 (2.3) |
| Redundancy | 11.2 (11.2) | 6.1 (6.0) | 10.3 (9.3) | 9.9 (8.8) | 7.3 (7.4) |
| Completeness (%) | 98.2 (96.9) | 99.8 (100.0) | 99.6 (99.9) | 99.6 (99.8) | 99.8 (99.9) |
| Refinement | |||||
| Resolution (Å) | 36.8–1.55 | 23.3–1.60 | 34.5–3.0 | 31.6–2.9 | 43.7–3.0 |
| No. of reflections | 40917 | 39805 | 17858 | 20515 | 18457 |
| Rwork/Rfree | 0.174/0.201 | 0.186/0.219 | 0.219/0.283 | 0.199/0.278 | 0.219/0.283 |
| Number of atoms | |||||
| Protein | 1,891 | 1,896 | 3,848 | 3,846 | 3,846 |
| RNA | — | — | 1,519 | 1,516 | 1,516 |
| AdoMet/Sinefungin | 27 | 27 | 54 | 54 | 54 |
| Water | 280 | 242 | — | — | — |
| B-factors (Å2) | |||||
| Protein | 20.1 | 22.3 | 89.7 | 64.6 | 79.2 |
| RNA | — | — | 104.7 | 88.4 | 104.6 |
| AdoMet/Sinefungin | 17.9 | 18.5 | 73.6 | 54.5 | 66.1 |
| Water | 34.4 | 32.9 | — | — | — |
| R.m.s. deviations | |||||
| Bond length (Å) | 0.020 | 0.014 | 0.008 | 0.022 | 0.018 |
| Bond angles (°) | 1.95 | 1.54 | 1.39 | 1.59 | 1.33 |
| Ramachandran plot | |||||
| Favored/allowed (%) | 99.1/0.9 | 99.2/0.8 | 97.7/2.1* | 97.9/2.1 | 97.9/2.1 |
| PDB ID code | 4YVG | 4YVH | 4YVI | 4YVJ | 4YVK |
Values in parentheses are for the highest-resolution shell.
*
One residue (Leu229 in subunit B) is plotted slightly outside the allowed region in Ramachandran plot.