Table S1.
Data collection and refinement statistics of X-ray crystallography
| apo-OsYchF1 at pH 6.5 (PDB ID code 5EE0) | apo-OsYchF1 at pH 7.85 (PDB ID code 5EE1) | AMPPNP-OsYchF1 (PDB ID code 5EE3) | GMPPNP-OsYchF1 (PDB ID code 5EE9) | |
| Data collection | ||||
| Wavelength, Å | 0.9795 | 0.9793 | 0.9790 | 0.9786 |
| Space group | P 1211 | P 22121 | P 212121 | P 212121 |
| Cell dimensions | ||||
| a, b, c, Å | 58.6, 66.9, 66.9 | 56.0, 70.4, 117.4 | 70.1, 112.4, 115.0 | 70.5, 112.1, 115.7 |
| α, β, γ, ° | 90.0, 112.7, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Resolution, Å | 50–2.21 (2.25–2.21) | 50–2.55 (2.59–2.55) | 50–2.90 (2.95–2.90) | 50–2.75 (2.80–2.75) |
| Rmerge, % | 7.7 (59.0) | 6.7 (80.0) | 8.0 (55.3) | 10.0 (48.4) |
| I/σ | 19.0 (2.0) | 17.2 (1.9) | 19.2 (1.9) | 12.6 (2.4) |
| Completeness, % | 97.4 (99.2) | 99.7 (99.9) | 99.9 (98.3) | 98.5(99.1) |
| Redundancy | 4.8 (4.1) | 5.4 (5.6) | 7.6 (5.5) | 4.5 (3.9) |
| Refinement | ||||
| Resolution, Å | 32.84–2.20 (2.26–2.20) | 50.01–2.53 (2.59–2.53) | 50.01–2.90 (2.97–2.90) | 50.01–2.75 (2.82–2.75) |
| No. of reflections | 17,505 (569) | 14,816 (754) | 19,709 (1346) | 22,711 (1384) |
| Rwork/Rfree, % | 23.5/25.8 | 22.9/26.3 | 22.7/26.1 | 22.9/26.2 |
| No. of atoms | ||||
| Protein | 2,832 | 2,791 | 5,496 | 5,433 |
| Ligands | — | — | 62 | 32 |
| Water | 112 | 23 | 18 | 256 |
| B factors | ||||
| Protein | 23.0 | 38.6 | 65.7 | 43.4 |
| Ligands | — | — | 87.1 | 54.5 |
| Water | 33.2 | 27.0 | 45.4 | 35.6 |
| rms deviations | ||||
| Bond lengths, Å | 0.007 | 0.01 | 0.009 | 0.005 |
| Bond angles, ° | 1.13 | 1.34 | 1.34 | 0.89 |
| Ramachandran plot,* % | 93.5/5.8/0.6/0.0 | 92.2/7.8/0/0 | 92.1/7.9/0/0 | 91.5/8.5/0/0 |
Values in parentheses are for highest-resolution shells.
*
Residues in: most favored, additional allowed, generously allowed, and disallowed regions of the Ramachandran plot, respectively.