Table 1. X-ray diffraction and structure determination statistics.
| PDB code | 3PF8 | 3PF9 | 3S2Z | 3PFB | 3QM1 | 3PFC |
| Enzyme | LJ0536 (wild-type) | LJ0536 S106A | LJ0536 S106A | LJ0536 S106A | LJ0536 S106A | LJ0536 S106A |
| Ligands | None | None | Caffeic acid (from soak of chlorogenic acid) | Ethyl ferulate, Form I | Ethyl ferulate, Form II | Ferulic acid |
| Data collection | ||||||
| Wavelength (Å) | Cu-Kα 1.54178 | Cu-Kα 1.54178 | Cu-Kα 1.54178 | Cu-Kα 1.54178 | Cu-Kα 1.54178 | Cu-Kα 1.54178 |
| Resolution (Å) | 50.0 – 2.35 | 50.0 – 1.75 | 50.0 – 1.75 | 50.0 – 10.0.58 | 23.80 – 1.82 | 50.0 – 1.75 |
| Space group | R32 | C2221 | C2 | C2 | C2221 | C2221 |
| Cell dimensions | ||||||
| a, b, c (Å) | 149.9, 149.9, 130.3 | 72.7, 85.7, 81.9 | 72.3, 84.2, 87.6 | 72.3, 83.9, 88.9 | 71.9, 85.4, 81.1 | 72.0, 85.4, 81.0 |
| a, b, g (°) | 90, 90, 120 | 90, 90, 90 | 90, 97.6, 90 | 90, 98.2, 90 | 90, 90, 90 | 90, 90, 90 |
| Number of observed reflections | 143192 | 140545 | 208914 | 101781 | 139955 | 146324 |
| Number of unique reflections | 23389 | 26002 | 51281 | 46265 | 22853 | 25396 |
| Rsym | 0.105 (0.442)a | 0.057 (0.460)b | 0.047 (0.462)c | 0.046 (0.260)d | 0.048 (0.327)e | 0.058 (0.484)f |
| I/σI | 13.44 (4.81) | 37.87 (3.75) | 21.86 (2.57) | 31.21 (3.09) | 27.56 (3.18) | 22.20 (2.88) |
| Completeness (%) | 99.0 (100.0) | 99.1 (96.1) | 99.7 (97.6) | 73.1 (21.6) | 100 (99.9) | 99.5 (94.0) |
| Redundancy | 6.1 (5.5) | 5.4 (4.1) | 4.1 (3.3) | 2.0 (1.3) | 6.1 (4.8) | 5.8 (5.1) |
| Refinement | ||||||
| Programs | Refmac, PHENIX, BUSTER | Refmac | Refmac | PHENIX, Refmac | PHENIX | PHENIX |
| Resolution (Å) | 31.49 – 2.34 | 50.0 – 1.75 | 50.0 – 1.76 | 44.20 – 1.58 | 23.07 – 1.82 | 17.65 – 1.75 |
| Number of reflections: working, test | 22192, 1194 | 23365, 1310 | 48659, 2615 | 47130, 2673 | 21234, 1119 | 23466, 1237 |
| Rwork/Rfree, 5% | 22.3/29.9 (27.3/36.5) | 14.1/19.9 (23.6/30.7) | 14.3/20.8 (19.0/28.2) | 21.1/30.4 (30.2/36.2) | 14.7/19.1 (22.8/26.7) | 14.7/17.9 (23.6/26.1) |
| No. atoms | ||||||
| Protein | 3836 | 1988 | 3935 | 3939 | 1991 | 1964 |
| Ligands | N/A | N/A | 26 | 32 | 16 | 14 |
| Solvent | 3 | 4 | 16 | 20 | 61 | 17 |
| Water | 146 | 275 | 432 | 907 | 173 | 224 |
| Average B-factors | ||||||
| Protein | 56.7 | 29.9 | 33.9 | 23.6 | 19.4 | 22.9 |
| Ligand | N/A | N/A | 35.9 | 33.0 | 19.1 | 21.8 |
| Solvent | 39.2 | 41.9 | 58.0 | 26.0 | 55.9 | 49.4 |
| Water | 44.9 | 43.3 | 46.7 | 39.2 | 31.5 | 24.4 |
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.010 | 0.025 | 0.023 | 0.021 | 0.016 | 0.016 |
| Bond angles (°) | 1.23 | 1.843 | 1.812 | 1.933 | 1.710 | 1.611 |
| Ramachandran analysis | ||||||
| Most favoured (%) | 86.4 | 89.1 | 89.3 | 88.4 | 90.8 | 90.7 |
| Additionally favoured (%) | 12.0 | 9.5 | 9.1 | 10.0 | 7.3 | 7.9 |
| Generously favoured (%) | 0.9 | 0.5 | 1.1 | 1.1 | 1.4 | 1.4 |
| Disallowed (%) | 0.7 | 0.9 | 0.5 | 0.5 | 0.5 | 0 |
a
Values in brackets refer to the highest resolution shell of 2.39 – 2.35 Å.
b
Values in brackets refer to the highest resolution shell of 1.78 – 1.75 Å.
c
Values in brackets refer to the highest resolution shell of 1.78 – 1.75 Å.
d
Values in brackets refer to the highest resolution shell of 1.61 – 1.58 Å.
e
Values in brackets refer to the highest resolution shell of 1.85 – 1.82 Å.
f
Values in brackets refer to the highest resolution shell of 1.78 – 1.75 Å.