Table 1.
Data collection and refinement statistics
| Data collection | RabGGTase Apo | RabGGTase–GGPP | RabGGTase–FPP |
|---|---|---|---|
| Wavelength (Å)a | 0.9800 | 1.0007 | 0.9998 |
| Resolution (highest shell, Å) | 29.2–1.8 (1.9–1.8) | 29.4–1.9 (2.0–1.9) | 29.4–1.9 (2.0–1.9) |
| Space group | P212121 | P212121 | P212121 |
| Cell constants (Å; deg) | a=66.7, b=90.6, c=114.1; α=β=γ=90 | a=67.3, b=90.6, c=114.5; α=β=γ=90 | a=66.9, b=90.9, c=114.2; α=β=γ=90 |
| VM | 2.5 | 2.5 | 2.5 |
| Total measurements | 294 558 | 257 863 | 313 284 |
| Unique reflections | 64 333 | 55 563 | 54 566 |
| Average redundancy | 4.6 (3.4) | 4.6 (4.5) | 5.7 (5.8) |
| I/σ | 16.4 (4.7) | 24.6 (5.4) | 22.5 (4.8) |
| Completeness (%) | 99.3 (99.7) | 99.4 (99.4) | 98.2 (98.1) |
| Rsymb | 6.3 (27.5) | 4.4 (30.8) | 4.6 (40.2) |
| Wilson B-factor (Å2) | 30 | 47 | 34 |
| Refinement | |||
| Resolution (highest shell, Å) | 1.8 (1.85–1.8) | 1.9 (1.95–1.9) | 1.9 (1.95–1.9) |
| Rc | 14.9 (16.3) | 18.0 (22.3) | 15.9 (18.6) |
| Rfreed | 19.4 (23.4) | 22.0 (28.8) | 21.6 (25.9) |
| r.m.s.d. bonds (Å)/angles (deg) | 0.009/1.250 | 0.010/1.375 | 0.010/1.409 |
| B-factor deviation bonds/angles (Å2) | |||
| Main chain | 1.157/1.860 | 0.936/1.497 | 1.119/1.820 |
| Side chain | 2.411/3.825 | 2.064/2.999 | 2.336/3.580 |
| Residues in Ramachandran core (%)e | 93.4 | 92.8 | 92.2 |
| Protein atoms Solvent atoms Ligand atoms | |||
| Average B-factor (Å2) | 18 | 37 | 25 |
| PDB accession code | 3DSS | 3DST | 3DSU |
| Data collection | RabGGTase–Ser-Cys- Ser-Cys(GG) | RabGGTase–Ser-Cys(GG)- Ser-Cys | RabGGTase–Ser-Cys(GG)-Ser-Cys(GG) |
| Wavelength (Å)a | 0.9999 | 0.9825 | 0.9841 |
| Resolution (highest shell, Å) | 29.4–2.1 (2.2–2.1) | 29.4–2.15 (2.25–2.15) | 29.4–2.1 (2.2–2.1) |
| Space group | P212121 | P212121 | P212121 |
| Cell constants (Å; deg) | a=67.0, b=90.6, c=114.4; α=β=γ=90 | a=67.1, b=90.9, c=114.3; α=β=γ=90 | a=67.4, b=91.2, c=114.6; α=β=γ=90 |
| VM | 2.5 | 2.5 | 2.5 |
| Total measurements | 763 680 | 153 685 | 302 144 |
| Unique reflections | 41 339 | 38 414 | 41 826 |
| Average redundancy | 18.5 (16.5) | 4.0 (4.1) | 7.2 (7.4) |
| I/σ | 31.0 (11.1) | 15.2 (5.2) | 23.4 (6.9) |
| Completeness (%) | 99.9 (99.7) | 99.1 (99.8) | 99.8 (100) |
| Rsymb | 8.5 (37.9) | 7.2 (37.3) | 5.7 (39.1) |
| Wilson B-factor (Å2) | 30 | 39 | 39 |
| Refinement | |||
| Resolution (highest shell, Å) | 2.1 (2.15–2.1) | 2.15 (2.2–2.15) | 2.1 (2.15–2.1) |
| Rc | 14.9 (14.0) | 17.0 (17.7) | 16.8 (17.0) |
| Rfreed | 21.1 (22.4) | 23.2 (27.4) | 23.0 (26.0) |
| r.m.s.d. bonds (Å)/angles (deg) | 0.011/1.456 | 0.012/1.446 | 0.011/1.285 |
| B-factor deviation bonds/angles (Å2) | |||
| Main chain | 1.100/1.968 | 1.391/2.440 | 1.166/1.867 |
| Side chain | 2.394/3.701 | 2.759/4.269 | 2.397/3.576 |
| Residues in Ramachandran core (%)e | 91.7 | 92.4 | 92.8 |
| Protein atoms Solvent atoms Ligand atoms | |||
| Average B-factor (Å2) | 26 | 36 | 30 |
| PDB accession code | 3DSV | 3DSW | 3DSX |
| aAll data were collected at beamline X10SA of the Swiss Light Source (Paul Scherrer Institute, Villigen, Switzerland). | |||
| bRsym=∑∑I(h)j−<I(h)>/∑∑I(h)j where I(h)j is the measured diffraction intensity and the summation includes all observations. | |||
| cR is the R-factor=(∑∣FO∣−∑∣FC∣)/∑∣FO∣. | |||
| dRfree is the R-factor calculated using 5% of the data that were excluded from the refinement. | |||
| eRamachandran core refers to the most favoured regions in the ϕ/ψ-Ramachandran plot. | |||