Table 1.
X-ray diffraction data collection and structure refinement statistics (set 1)
| NAC state* (PDB ID code) | ||||
| C1S1 (5F8G) | C1S1/2 (5F8H) | C1S2/3 (5F8I) | C1S4 (5F8J) | |
| Data collection† | ||||
| Space group | P212121 | P212121 | P212121 | P212121 |
| Cell dimensions | ||||
| a, b, c, Å | 63.1, 77.6, 153.6 | 63.3, 77.1, 149.9 | 63.7, 77.3, 149.7 | 63.4, 76.6, 149.3 |
| α, β, γ, ° | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution, Ň | 60.0–2.78 (2.88–2.78) | 60.0–2.45 (2.54–2.45) | 60.0–2.50 (2.59–2.50) | 60.0–2.66 (2.76–2.66) |
| Rmerge | 0.117 (0.50) | 0.062 (0.51) | 0.060 (0.48) | 0.073 (0.50) |
| I/σI | 13.6 (3.2) | 21.4 (3.3) | 20.1 (2.9) | 17.7 (2.5) |
| Completeness, % | 97.6 (98.4) | 99.7 (99.9) | 99.6 (100.0) | 98.1 (96.4) |
| Redundancy | 5.4 (5.5) | 4.7 (4.8) | 4.3 (4.3) | 4.9 (4.9) |
| Refinement | ||||
| Resolution, Å | 2.78 | 2.45 | 2.50 | 2.66 |
| No. reflections | 19,258 | 27,772 | 26,095 | 20,430 |
| Rwork/Rfree§, % | 19.3/24.2 | 19.8/24.4 | 19.9/24.4 | 18.3/22.8 |
| No. atoms | ||||
| Protein/RNA | 3,681/471 | 3,681/471 | 3,681/471 | 3,685/491 |
| Ligand/ion/water | –/ 1/115 | 5/2/141 | 40/3/144 | 25/3/111 |
| B-factors | ||||
| Protein/RNA | 42.6/53.2 | 52.3/60.8 | 57.5/72.2 | 50.4/62.8 |
| Ligand/ion/water | –/18.6/38.9 | 36.3/44.4/49.8 | 53.0/53.2/55.5 | 43.6/39.1/48.1 |
| RMSD | ||||
| Bond lengths, Å | 0.008 | 0.008 | 0.008 | 0.008 |
| Bond angles, ° | 1.13 | 1.13 | 1.12 | 1.17 |
| Ramachandran statistics¶ | 91.2/8.3/0.2/0.2 | 93.1/6.6/0.0/0.2 | 92.9/6.9/0.0/0.2 | 92.6/6.9/0.2/0.2 |
*
Coding scheme: C, cycle; S, state; subscript numbers reflect the cycle and state numbers: x/(x+1) indicates an NAC species between state x and the next reference state. Soaking strategy: C1S1/2: CTP for 4 min; C1S2/3 – CTP for 4 min, and then transfer to UTP for 10 min; C1S4: CTP for 5 min 10 s.
†
One crystal was used for data collection for each structure.
‡
Values in parentheses are for highest-resolution shell.
§
5% of data are taken for the Rfree set, and the same Rfree set is applied for all structures.
¶
Values are in percentage and are for most favored, additionally allowed, generously allowed, and disallowed regions in Ramachandran plots, respectively.