Table 2. Structure determination and model refinement.
Values in parentheses are for the highest resolution shell.
| Aae Hfq, apo form (‘P1’) | Aae Hfq·U6 RNA (‘P6’) | |
|---|---|---|
| Resolution range (Å) | 46.35–1.49 (1.51–1.49) | 34.21–1.50 (1.56–1.50) |
| Completeness (%) | 93.9 | 94.9 |
| No. of reflections, working set | 138104 (12739) | 13171 (1308) |
| No. of reflections, test set | 10625 (983) | 662 (70) |
| Final R cryst | 0.1323 (0.1531) | 0.1443 (0.1499) |
| Final R free | 0.1696 (0.2108) | 0.1719 (0.1933) |
| No. of non-H atoms | ||
| Macromolecules | 7670 Hfq | 598 Hfq, 43 RNA |
| Ligands | 200 MPD, 32 Gnd, 7 Cl−, 28 PEG | 8 MPD, 7 PEG |
| Solvent | 413 H2O | 36 H2O |
| Total | 8350 | 692 |
| No. residues of protein, solvent or ligand molecules included in the final, refined structure | ||
| Aae Hfq | 848 [over 12 subunits] | 71 [over 1 subunit] |
| H2O | 413 | 36 |
| U6 RNA | ∼2–3† | |
| MPD | 25 | 1 |
| Cl− | 7 | |
| Gnd | 8 | |
| PEG‡ | 4 | 1 |
| R.m.s. deviations | ||
| Bonds (Å) | 0.005 | 0.005 |
| Angles (°) | 0.75 | 0.76 |
| Average B factors (Å2) | ||
| Protein | 19.32 | 22.18 |
| Ligand | 25.89 | 30.44 |
| Ramachandran plot | ||
| Most favored (%) | 98 | 97 |
| Allowed (%) | 1.7 | 2.9 |
| Outliers (%) | 0 | 0 |
| Rotamer outliers (%) | 0.34 | 1.5 |
| PDB code | 5szd | 5sze |
†
This value is given as a range because two complete U nucleotides, plus a fragment of a third residue, could be built into the electron-density maps.
‡
Fragments of polyethylene glycol could be built in both structures, generally of two to three repeat units [i.e. (O–C–C)2–O, neglecting H atoms].