Data collection and refinement statistics.
| Molecule name | SeMet SH3BP5-RA/M167A | SeMet SH3BP5-RA/M167A | Native SH3BP5-RA | SH3BP5–Rab11a |
|---|---|---|---|---|
| PDB ID | 6IXE | 6IXF | 6IXG | 6IXV |
| Data collection | ||||
| Beamline | SPring-8 BL41XU | SPring-8 BL41XU | SPring-8 BL41XU | SPring-8 BL41XU |
| Space group | I41 | P41 | P41 | I222 |
| Cell constants | ||||
| a, b, c (Å) | 79.3, 79.3, 108.1 | 78.3, 78.3, 93.0 | 80.1, 80.1, 95.0 | 117.8, 199.1, 303.9 |
| α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Resolution | 50–3.35 (3.41–3.35) | 50–3.6 (3.66–3.6) | 50–3.8 (3.87–3.8) | 50–3.8 (3.87–3.8) |
| Rsym | 0.158 (0.357) | 0.181 (0.704) | 0.187 (0.707) | 0.157 (1.546) |
| I/σI | 30.0 (2.52) | 14.9 (1.04) | 14.9 (1.42) | 41.1 (1.32) |
| Redundancy | 8.2 (3.2) | 8.2 (3.9) | 9.1 (5.1) | 32.6 (16.4) |
| Completeness (%) | 96.9 (89.0) | 97.5 (92.3) | 94.4 (80.1) | 100.0 (100.0) |
| Refinement | ||||
| Resolution (Å) | 38.9–3.35 | 47.5–3.6 | 40–3.8 | 49.8–3.8 |
| No. reflections | 4,689 | 6,398 | 5,578 | 35,564 |
| Rwork/Rfree | 0.269/0.314 | 0.234/0.261 | 0.242/0.278 | 0.229/0.259 |
| No. atoms | ||||
| Protein | 1,737 | 3,613 | 3,577 | 12,750 |
| Ligand/ion | 8 | 0 | 0 | 15 |
| B-factors (Å2) | ||||
| Protein | 122.7 | 119.3 | 140.2 | 224.9 |
| Ligand/ion | 127.3 | — | — | 270.9 |
| Rmsds | ||||
| Bond lengths (Å) | 0.003 | 0.003 | 0.003 | 0.001 |
| Bond angles (°) | 0.658 | 0.604 | 0.678 | 0.461 |
| Ramachandran plot | ||||
| Favored (%) | 99.0 | 97.5 | 99.5 | 97.0 |
| Allowed (%) | 1.0 | 2.5 | 0.5 | 3.0 |
| Outliers (%) | 0.0 | 0.0 | 0.0 | 0.0 |