Table 1.
Summary of diffraction data and structure refinement statistics
| Rabex-5CC | Rabex-5CC-Rabaptin-5C212 | Rabex-5Δ-Rabaptin-5C212 | Rab5-Rabex-5Δ-Rabaptin-5C212 | |
|---|---|---|---|---|
| Diffraction data | ||||
| Wavelength (Å) | 0.9200 | 1.0000 | 0.9793 | 0.9785 |
| Space group | P21 | C2 | P3121 | P41212 |
| Cell parameters | ||||
| a (Å) | 46.8 | 90.0 | 87.2 | 174.8 |
| b (Å) | 40.3 | 28.9 | 87.2 | 174.8 |
| c (Å) | 51.6 | 108.0 | 168.9 | 149.0 |
| α (°) | 90.0 | 90.0 | 90.0 | 90.0 |
| β (°) | 95.1 | 102.2 | 90.0 | 90.0 |
| γ (°) | 90.0 | 90.0 | 120.0 | 90.0 |
| Resolution (Å) | 50.0–2.00 | 50.0–2.20 | 50.0–3.10 | 50.0–4.60 |
| (2.07–2.00)* | (2.28–2.20) | (3.21–3.10) | (4.76–4.60) | |
| Observed reflections | 38,445 | 47,482 | 79,255 | 124,340 |
| Unique reflections (I/σ(I) > 0) | 12,748 | 13,816 | 13,730 | 12,699 |
| Average redundancy | 3.0 (3.0) | 3.4 (3.0) | 5.8 (6.0) | 9.8 (9.0) |
| Average I/σ(I) | 23.6 (14.0) | 21.2 (3.4) | 20.1 (2.4) | 18.2 (2.8) |
| Completeness (%) | 96.4 (97.7) | 97.7 (85.8) | 98.1 (100.0) | 97.6 (95.8) |
| Rmerge (%)† | 5.3 (9.3) | 6.0 (28.0) | 8.2 (64.3) | 11.7 (94.3) |
| Refinement and structure model | ||||
| Reflections (Fo ≥ 0σ(Fo)) | ||||
| Working set | 11,437 | 12,433 | 10,806 | 11,982 |
| Test set | 622 | 691 | 601 | 631 |
| Rwork/Rfree (%)‡ | 19.1/23.4 | 19.3/23.5 | 26.4/31.5 | 25.1/34.3 |
| No. of atoms | 1726 | 1814 | 3074 | 9679 |
| Protein | 1621 | 1627 | 3074 | 9679 |
| Water | 105 | 187 | – | – |
| Average B factor (Å2) | ||||
| All atoms | 22.8 | 58.5 | 72.0 | 187.3 |
| Main-chain atoms | 17.9 | 51.8 | 72.6 | 186.9 |
| Side-chain atoms | 25.9 | 64.0 | 70.7 | 187.7 |
| Water | 34.9 | 63.5 | - | - |
| RMS deviations | ||||
| Bond lengths (Å) | 0.018 | 0.014 | 0.005 | 0.015 |
| Bond angles (°) | 1.61 | 1.37 | 1.27 | 1.87 |
| Ramachandran plot (%) | ||||
| Most favored | 99.5 | 99.5 | 92.1 | 93.8 |
| Allowed | 0.5 | 0.5 | 7.6 | 5.8 |
| Generously allowed | 0.0 | 0.0 | 0.3 | 0.5 |
*
Numbers in parentheses represent the highest resolution shell.
†
Rmerge = ∑hkl∑i|Ii(hkl)i−<I(hkl)>|/∑hkl∑iIi(hkl).
‡
R = ∑hkl‖Fo|−|Fc‖/∑hkl|Fo|.