Table 1.
Data collection and refinement statistics of the ST1710 native, salicylate, DNA complex and their mutants
| Data collection | ST1710-salicylate | ST1710-native | ST1710–DNA complex |
R89A | R90A | K91A | ||
|---|---|---|---|---|---|---|---|---|
| Peak | Edge | Remote (Low energy) | ||||||
| Wavelength | 1.54178 | 1.54178 | 0.97896 | 0.97930 | 1.000 | 1.54178 | 1.54178 | 1.54178 |
| Space group | P41212 | P41212 | C2221 | P41212 | P41212 | P41212 | ||
| Cell dimensions (Å) | a = b = 46.14, c = 137.64 | a = b = 46.04, c = 138.45 | a = 94.44, b = 106.73, c = 82.26 | a = b = 45.86, c = 138.17 | a = b = 45.90, c = 137.42 | a = b = 45.96, c = 138.29 | ||
| No. of molecules/asu | 1 | 1 | 2 | 1 | 1 | 1 | ||
| Resolution Range (Å) | 40–1.80 (2.07–2.0)a | 40–2.0 (2.07–2.0) | 50–2.10 (2.18–2.10) | 40–2.20 (2.28–2.20) | 40–1.90 (1.97–1.90) | 50–2.10 (2.18–2.10) | ||
| Unique reflections | 13 381 | 10 380 | 24 349 | 24 204 | 24 231 | 8143 | 12 085 | 9163 |
| Redundancy | 13.4 (7.6) | 18.5 (19.1) | 9.6 (9.8) | 12.5 (13.0) | 13.0 (12.6) | 12.2 (12.9) | ||
| Completeness (%) | 91.3 (99.8) | 96.0 (94.4) | 99.1 (98.7) | 99.1 (98.8) | 99.0 (98.6) | 100 (100) | 97.7 (95.1) | 98.1 (100) |
| Rmergeb | 0.100 (0.264) | 0.104 (0.321) | 0.080 (0.294) | 0.072 (0.284) | 0.067 (0.281) | 0.091 (0.389) | 0.065 (0.326) | 0.095 (0.302) |
| Refinement statistics | ||||||||
| Resolution Range (Å) | 20–1.80 | 20–2.0 | 20.0–2.10 | 20–2.20 | 20–1.90 | 20.0–2.10 | ||
| Reflections used in the refinement | 13 138 | 10 244 | 24 202 | 7877 | 11 906 | 8997 | ||
| Total no. of reflections used for working set | 12 246 | 9423 | 22 476 | 7292 | 10 943 | 8258 | ||
| Rworkc | 0.233 | 0.211 | 0.237 | 0.201 | 0.205 | 0.218 | ||
| Total no. of reflections used for Rfree | 892 | 821 | 1726 | 585 | 963 | 739 | ||
| Rfreed | 0.265 | 0.252 | 0.287 | 0.245 | 0.239 | 0.270 | ||
| No. of protein atoms | 1142 | 1142 | 2305 | 1136 | 1136 | 1138 | ||
| No. of nucleic acid atoms | – | – | 466 | |||||
| No. of water molecules | 152 | 156 | 154 | 125 | 160 | 127 | ||
| No. ligand molecules | 1 | |||||||
| No. Ca2+ ions | – | 1 | – | 1 | 1 | 1 | ||
| Average B factor (Å2) | 29.6 | 31.8 | 51.2 | 28.1 | 33.5 | 36.9 | ||
| Ramachandran statistics | ||||||||
| Most favored regions (%) | 97.7 | 98.5 | 98.1 | 97.0 | 97.7 | 96.2 | ||
| Allowed regions (%) | 2.3 | 1.5 | 1.9 | 3.0 | 2.3 | 3.8 | ||
| PDB code | 3GEZ | 3GF2 | 3GFI | 3GFJ | 3GFL | 3GFM | ||
RMSD in bond angles and bond lengths are varied from 0.005 to 0.007 (Å) and 1.0–1.1 (°). Solvent content is about 55%.
aValues in parentheses are for the highest resolution shell.
bRmerge = ∑h ∑i | I(h, i)−<I(h)> | /∑h ∑i I(h, i), where I(h, i) is the intensity value of the ith measurement of h and <I(h)> is the corresponding mean value of I(h) for all i measurements.
cR factor = ∑ | |Fobs|−|Fcalc| |/|Fobs|, where |Fobs| and |Fcalc| are the observed and calculated structure factor amplitudes, respectively.
dRfree is the same as R factor, but for a 5–7% subset of all reflections.