Table 1.
SAXS-derived three-dimensional parameters for the six RcRE RNA variants described in this study.
| RcRE variant | Length (nucleotides) | Theoretical MW (kDa) | MW by SAXS (kDa) | Rg, Guinier (Å) | Rg, Real Space (Å) | Depth* (Å) | Width* (Å) | Dmax (Å) |
|---|---|---|---|---|---|---|---|---|
| 433-mer RcRE | 433 | 140.4 | 131.7 | 75±4 | 80±1 | ~28 | ~70 | 282 |
| Truncated (Tr) | 313 | 102.0 | 107.0 | 61±1 | 60 ± 1 | 23 | 62 | 218 |
| TrΔSLIII | 271 | 87.9 | 89.8 | 53±1 | 53.0 ± 0.8 | 25 | 60 | 192 |
| TrΔSLIIab | 265 | 86.2 | 87.7 | 50.2 ± 0.8 | 53.1 ± 0.7 | 25 | 62 | 185 |
| TrΔSLIII,IIf | 239 | 77.2 | 83.5 | 52±1 | 53.4±0.9 | 24 | 56 | 183 |
| TrΔSLIIc | 259 | 84.2 | 79.2 | 49±1 | 51.9±0.6 | 23 | 57 | 181 |
Rg Guinier and Rg in Real Space were produced from Guinier plots and GNOM, respectively. The radius of gyration (Rg, the radius about the axis of rotation of the molecule) was generated from Guinier plot of the data extrapolated to infinite dilution in the range of qRg < 1.3
Dmax, the molecule’s maximum dimension was calculated in GNOM.
*
Values estimated based on the P(r) function.
The molecular weight (MW) was obtained by sequence (theoretical) and by SAXS based on the correlation volume, Vc. Qmax in the range of 0.2–0.3 Å−1 was used for the estimation.