Table 2. Average and standard deviations in parentheses of RMSd in Å between the final theoretical molecular models, computed from a continuous and flexible thin rod model or ‘BCE’ model, versus published molecular conformations deposited in the PDB.
| PDB identification |
Main backbone atoms |
Main backbone atoms without Nc |
All atoms |
All atoms without Nc |
||||
|---|---|---|---|---|---|---|---|---|
| Loop | Stem + loop | Loop | Stem + loop | Loop | Stem + loop | Loop | Stem + loop | |
| DNA | ||||||||
| 1ac7 | 1.29 (0.07) | 1.22 (0.13) | 0.98 (0.06) | 0.98 (0.15) | 1.62 (0.10) | 1.35 (0.10) | 0.97 (0.09) | 0.92 (0.11) |
| 1bjh | 0.91 (0.01) | 1.19 (0.01) | 0.37 (0.00) | 0.99 (0.01) | 1.57 (0.00) | 1.38 (0.01) | 1.27 (0.01) | 1.24 (0.01) |
| 1xue | 0.67 (0.00) | 1.22 (0.01) | 0.20 (0.00) | 1.07 (0.01) | 1.27 (0.00) | 1.34 (0.01) | 0.97 (0.00) | 1.22 (0.01) |
| 1zhu | 0.76 (0.13) | 1.15 (0.03) | 0.32 (0.05) | 1.04 (0.05) | 1.31 (0.05) | 1.32 (0.02) | 1.08 (0.03) | 1.21 (0.03) |
| RNA | ||||||||
| 1aud | 1.01 (0.11) | 1.09 (0.23) | 0.92 (0.12) | 1.03 (0.21) | 1.94 (0.24) | 1.70 (0.19) | 1.74 (0.29) | 1.55 (0.18) |
| 1b36 | 1.56 (0.12) | 1.36 (0.10) | 1.26 (0.13) | 1.05 (0.11) | 2.11 (0.10) | 1.73 (0.09) | 1.54 (0.12) | 1.28 (0.10) |
| 1c0o | 1.36 (0.04) | 1.24 (0.04) | 1.10 (0.03) | 0.97 (0.03) | 1.92 (0.04) | 1.64 (0.04) | 1.43 (0.03) | 1.26 (0.04) |
| 1hlx | 1.29 (0.07) | 1.20 (0.07) | 1.15 (0.05) | 1.10 (0.08) | 1.89 (0.08) | 1.55 (0.08) | 1.62 (0.11) | 1.37 (0.11) |
Different sets of atoms are taken into account in the RMSd computations with the following notations: ‘All atoms’ are all nucleotides atoms; ‘Main backbone atoms’ are: P, O5′, C5′, C4′, C3′, O3′; the ‘stem’ includes the first two base pairs below the loop. In columns ‘without Nc’, the third nucleotide, Nc, is not included in the computations.