TABLE 1.
Crystallographic statistics of AcHcaR and its complexes with ligands and the cognate DNA
Mol, molecules; AU, asymmetric unit; FOM, figure of merit; COU, coumaric acid; FLA, ferulic acid; VLN, vanillin.
| Apo-AcHcaR | AcHcaR + coumaric acid | AcHcaR + ferulic acid | AcHcaR + vanillin | AcHcaR + DHBA | AcHcaR-DNA peak | AcHcaR-DNA inflection | AcHcaR-DNA high remote | |
|---|---|---|---|---|---|---|---|---|
| Data collection | ||||||||
| Space group | P21212 | P21212 | P21212 | P21212 | P21212 | P61 | P61 | P61 |
| Unit cell (Å) | 63.26, 80.54, 63.06 | 64.02, 83.63, 63.06 | 63.67, 82.81, 63.17 | 63.68, 82.82, 63.03 | 63.58, 83.10, 63.05 | a = b = 161.97, 73.83 | a = b = 162.29, 73.89 | a = b = 161.28, 74.09 |
| Molecular mass (Da) (residues) | 33,058 (287)a | 33,058 (287)a | 33,058 (287)a | 33,058 (287)a | 33,058 (287)a | 33,058 (287)a/7,450 (24)b | ||
| Mol (AU) | 2 | 2 | 2 | 2 | 2 | 2 complexesc | ||
| Wavelength (Å) | 0.9794 | 0.9794 | 0.9794 | 0.9794 | 0.9794 | 0.9792 | 0.9794 | 0.9716 |
| Resolution (Å) | 49.8–2.35 | 39.6–2.30 | 29.5–1.89 | 39.4–2.30 | 34.8–2.1 | 50–3.05 (3.05–3.10) | 50–3.00 (3.00–3.05) | 50–3.10 (3.10–3.15) |
| Number of reflections | 13,890/673d | 15,489/747e | 26,574/1,121f | 15,395/738g | 20,059/983h | 20,971/1,710i | 22,204/1,843i | 19,822/1,625i |
| Redundancy | 6.1/5.6 | 7.9/8.1 | 7.3/4.8 | 7.9/8.1 | 7.9/7.7 | 6.0/5.7i | 6.6/6.2i | 7.1/6.4i |
| Completeness (%) | 99.8/100 | 99.7/100 | 97.3/83.0 | 99.9/100 | 99.9/99.8 | 99.3/99.4i | 99.4/99.4i | 99.6/99.9i |
| Rmerge | 0.107/0.674 | 0.090/0.499 | 0.063/0.337 | 0.098/0.674 | 0.098/0.638 | 0.071/0.607i | 0.056/0.736i | 0.110/0.583i |
| I/σ(I) | 9.2/3.3 | 14.1/5.1 | 15.7/4.4 | 10.8/3.7 | 3.5 | 21.1/3.0i | 24.6/2.4i | 12.1/4.0i |
| Phasing | SAD | SAD | SAD | SAD | SAD | MAD | ||
| Phasing power | 1.32 | 2.00 | 1.56 | 1.67 | 1.73 | 1.32/1.14j | ||
| FOM | 0.22 | 0.36 | 0.31 | 0.30 | 0.33 | 0.776 | ||
| Refinement | ||||||||
| Resolution (Å) | 49.8–2.35 | 39.6–2.30 | 29.5–1.89 | 39.4–2.30 | 34.8–2.10 | 38.9–3.00 | ||
| Reflections (work/test) | 25,693/1,274k | 15,439/767 | 26,262/1,325 | 15,337/766 | 19,862/1,014 | 20,010/992 | ||
| Rcrystal/Rfree | 0.187/0.253 | 0.174/0.213 | 0.176/0.206 | 0.167/0.225 | 0.173/0.215 | 0.255/0.294 | ||
| r.m.s.d. bond (Å)/angle (°) | 0.013/1.27 | 0.002/0.618 | 0.006/0.947 | 0.007/1.00 | 0.007/0.920 | 0.004/0.696 | ||
| Protein residues | 12–150, 10–153 | 11–150, 11–153 | 11–153, 11–154 | 11–150, 11–153 | 11–149, 11–152 | 12–150 × 4 | ||
| Solvent/ligand | 67/1 SO4 | 117/2 COU | 166/2 FLA | 86/2 VLN | 183/2 DHBA | −12–11 × 4l | ||
| Wilson B/mean B (Å2) | 47.5/67.2 | 44.1/49.5 | 32.7/47.9 | 44.3/47.5 | 35.1/42.7 | 90.18/173.4 | ||
| Ramachandran plot | ||||||||
| Most favored/disallowed (%) | 91.7/0.0 | 99.6/0.0 | 100.0/0.0 | 98.18/0.0 | 99.64/0.0 | 97.3/0.18 | ||
a Not including cloning artifact.
b DNA.
c Protein-DNA complex.
d Last resolution bin, 2.39–2.35 Å.
e Last resolution bin, 2.34–2.30 Å.
f Last resolution bin, 1.93–1.89 Å.
g Last resolution bin, 2.34–2.30 Å.
h Last resolution bin, 2.14–2.10 Å.
i Highest resolution bin.
j Anomalous/dispersive.
k Including Bijvoet pairs.
l DNA residues.