Table 2. Summary of diffraction data and structure refinement statistics.
SAM-bound | SAH-bound | Apo (V66W/E67P) | |
Diffraction data | |||
Wavelength (Å) | 0.9793 | 0.9792 | 0.9792 |
Space group | P1 | P1 | I23 |
Cell parameters | |||
a (Å) | 50.27 | 49.93 | 168.49 |
b (Å) | 64.10 | 63.99 | 168.49 |
c (Å) | 79.27 | 80.27 | 168.49 |
α (°) | 90.10 | 90.26 | 90 |
β (°) | 93.27 | 93.38 | 90 |
γ (°) | 96.61 | 96.79 | 90 |
Resolution (Å) | 43.32–2.10 | 49.49–2.09 | 37.68–3.55 |
(2.15–2.10)* | (2.14–2.09) | (3.68–3.55) | |
Observed reflections | 213,131 | 108,874 | 59,066 |
Unique reflections (I/σ(I) > 0) | 51,008 | 54,989 | 9792 |
Average redundancy | 4.2 (4.2) | 2.0 (2.0) | 6.0 (6.3) |
Average I/σ(I) | 9.5 (1.8) | 6.1 (1.7) | 7.9 (1.5) |
Completeness (%) | 88.5 (59.6) | 94.8 (78.5) | 99.8 (100.0) |
Rmerge (%)† | 12.7 (84.1) | 10.5 (54.0) | 16.8 (81.3) |
CC1/2 | 0.995 (0.602) | 0.993 (0.678) | 0.992 (0.686) |
Refinement and structure model | |||
Reflections [Fo ≥ 0σ(Fo)] | |||
Working set | 48,879 | 52,979 | 9236 |
Test set | 2,018 | 1,995 | 485 |
Rwork/Rfree (%)‡ | 18.8 / 23.9 | 16.6 / 20.7 | 22.5/27.4 |
No. of protein atoms | 7,005 | 7,176 | 3843 |
No. of ligand atoms | 108 | 104 | – |
No. of water atoms | 427 | 598 | – |
Average B factor (Å2) | |||
All atoms | 29.6 | 26.5 | 93.2 |
Protein | 29.4 | 26.0 | 93.2 |
Ligand | 22.9 | 16.3 | – |
Water | 31.1 | 32.1 | – |
RMSD | |||
Bond lengths (Å) | 0.008 | 0.007 | 0.008 |
Bond angles (°) | 1.0 | 0.9 | 1.2 |
Ramachandran plot (%) | |||
Favored | 96.8 | 97.6 | 94.3 |
Allowed | 3.2 | 2.4 | 5.7 |
Disallowed | 0.0 | 0.0 | 0.0 |
*Numbers in parentheses refer to the highest-resolution shell.
†Rmerge = ∑hkl∑i|Ii(hkl)i − 〈I(hkl)〉|/∑hkl∑iIi(hkl).
‡R factor = ||Fo| − |Fc||/|Fo|.