TABLE 1.
Data collection and refinement statistics
| SeMet | Native (unliganded) | WT·RuBP complex | C133S·α-R15P complex | |
|---|---|---|---|---|
| Data collection | ||||
| Space group | P212121 | P212121 | P212121 | P41212 |
| Cell dimensions (a, b, c) (Å) | 117.4, 130.9, 132.8 | 117.3, 130.8, 132.8 | 117.3, 130.6, 132.7 | 146.5, 146.5, 99.6 |
| X-ray source | PF BL-17A | SPring-8 BL41XU | PF BL-5A | PF AR NW12A |
| Wavelength (Å) | 0.97896 | 1.0000 | 1.0000 | 1.0000 |
| Resolution (Å)a | 50-2.70 (2.80-2.70) | 50-2.50 (2.59-2.50) | 50-2.60 (2.69-2.60) | 50-2.85 (2.95-2.85) |
| Total reflections | 424,789 | 510,338 | 454,465 | 376,565 |
| Unique reflections | 56,920 | 71,476 | 63,161 | 26,012 |
| Completeness (%)a | 100.0 (100.0) | 100.0 (99.8) | 99.9 (100.0) | 100.0 (100.0) |
| 〈I〉/〈σ(I)〉a | 17.3 (6.2) | 26.3 (4.7) | 23.8 (4.6) | 20.1 (5.6) |
| Rsyma,b | 0.093 (0.330) | 0.071 (0.396) | 0.076 (0.377) | 0.129 (0.462) |
| Phasing | SADc | |||
| Resolution (Å) | 50-2.70 | |||
| Figure of merit after SOLVE | 0.46 (∼3.4 Å) | |||
| Figure of merit after RESOLVE | 0.67 | |||
| Refinement | ||||
| Resolution (Å) | 43.66-2.50 (2.66-2.50) | 43.64-2.60 (2.76-2.60) | 45.97-2.85 (3.03-2.85) | |
| Rwork/Rfreed | 0.204/0.266 | 0.201/0.255 | 0.201/0.262 | |
| No. of atoms | ||||
| Protein, Water, Mg, Cl, PEG | 15183, 308, 2, 0, 42 | 15368, 268, 2, 0, 42 | 7635, 153, 2, 3, 83 | |
| RuBP or α-R15P | 108 | 54 | ||
| Average B-factors | ||||
| Protein, Water, Mg, Cl, PEG (Å2) | 45.8, 33.3, 54.1, −, 56.3 | 43.3, 31.2, 48.6, −, 56.7 | 28.4, 20.7, 35.9, 39.5, 47.7 | |
| RuBP or α-R15P (Å2) | 38.0 | 24.1 | ||
| r.m.s. deviation bond length (Å) | 0.006 | 0.007 | 0.009 | |
| r.m.s. deviation bond angles (degrees) | 1.20 | 1.20 | 1.30 | |
| Ramachandran analysisd | ||||
| Favored, allowed, outliers (%) | 95.5, 4.3, 0.2 | 96.1, 3.9, 0.0 | 95.1, 4.8, 0.1 | |
| Protein Data Bank entry | 3A11 | 3A9C | 3VM6 | |
a Values in parentheses are for the highest resolution shell.
b Rsym = ΣhklΣi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣiIi(hkl), where Ii(hkl) is the ith intensity measurement of reflection hkl, and 〈I(hkl)〉 is the mean intensity obtained from multiple observations of symmetry-related reflections.
c Single-wavelength anomalous dispersion.
d Rwork = Σ‖Fo| − |Fc|/Σ|Fo|. Rfree is the same as Rwork but for the 5% subset of all reflections that were never used in crystallographic refinement.
d Calculated by MolProbity.