Table 3.
Data collection and refinement statistics in Se-DNA, Se-Br-DNA and Br-DNA structures
| Structure (PDB ID) | Se-DNA (1Z7I) | Se-Br-DNA (2D LJ) | Se-Br-DNA (2GPX) | Br-DNA (2H05) |
|---|---|---|---|---|
| Data collection | ||||
| Space group | P43212 | P43212 | P43212 | P43212 |
| Cell dimensions: a = b, c (Å), | 42.076, 23.935 | 42.369, 23.744 | 42.252, 24.133 | 42.048, 24.270 |
| Resolution range Å (last shell) | 50.00–1.28 (1.36–1.28) | 50.00–1.50 (1.55–1.50) | 50.00–1.60 (1.66–1.60) | 50.00–1.80 (1.86–1.80) |
| Unique reflections | 6325 (552) | 3777 (354) | 3161 (297) | 2248 (203) |
| Completeness % | 95.3 (70.0) | 99.7 (99.2) | 99.7 (99.3) | 99.4 (95.8) |
| Rmerge % | 8.0 (32.8) | 5.1 (27.8) | 8.4 (49.9) | 4.5 (32.3) |
| I/σ(I) | 14.8 (4.3) | 14.4 (4.9) | 13.1 (4.2) | 12.1 (2.7) |
| Redundancy | 12.4 (10.7) | 12.3 (9.1) | 12.4 (9.0) | 12.1 (7.1) |
| Refinement | ||||
| Resolution range Å (last shell) | 20.81–1.28 (1.36–1.28) | 18.16–1.50 (1.59–1.50) | 18.90–1.60 (1.70–1.60) | 18.81–1.80 (1.91–1.80) |
| Rwork % | 17.7 (23.7) | 18.3 (18.9) | 18.7 (21.3) | 21.3 (27.3) |
| Rfree % | 20.0 (23.1) | 22.8 (22.7) | 23.8 (24.4) | 24.8 (41.3) |
| Number of reflections | 5275 (552) | 3597 (473) | 2909 (289) | 2036 (247) |
| Number of atoms | ||||
| Nucleic Acid (single) | 161 | 160 | 160 | 160 |
| Heavy-atoms and ion | 1 Se | 1 Se, 1 Br | 1 Se, 1 Br, 1 Ba2+ | 1 Br |
| Water | 44 | 43 | 31 | 33 |
| R.m.s.d | ||||
| Bond length Å | 0.012 | 0.011 | 0.010 | 0.009 |
| Bond angle | 1.8 | 1.6 | 1.8 | 1.9 |
| Average B-factors Å2 | ||||
| All atoms | 15.0 | 18.8 | 25.9 | 32.5 |
| Wilson plot | 14.9 | 18.2 | 23.6 | 29.8 |
| Overall anisotropic B-values | ||||
| B11/B22/B33 | 0.70/0.70/−1.41 | −0.29/−0.29/0.58 | 0.31/0.31/−0.62 | 2.20/2.20/−4.41 |
| Bulk solvent correction | ||||
| Solvent density e/Å3 | 0.30 | 0.32 | 0.34 | 0.32 |
| B-factors Å2 | 22.2 | 34.5 | 40.05 | 41.04 |
| Coordinates error (c.-v.) 5Å | ||||
| Esd. from Luzzatt plot Å | 0.15 | 0.19 | 0.22 | 0.23 |
| Esd. from SIGMAA Å | 0.10 | 0.05 | 0.12 | 0.20 |
Rmerge = Σ|I − <I>|/ΣI.