Table 1. Statistics of X-ray crystallographic data collection and model refinement.
| Data collection | ||||
|---|---|---|---|---|
| Dataset | EphA2/SHIP2 | EphA6/Odin | EphA5/SAMD5 | |
| Space group | C2 | P212121 | C2 | |
| Unit cell (a, b, c, Å) | 138.283, 43.344, 46.377 | 38.985, 85.042, 98.383 | 98.195, 29.651, 54.170 | |
| Unit cell (α, β, γ, °) | 90, 95.354, 90 | 90, 90, 90 | 90, 109.952, 90 | |
| Wavelength (Å) | 0.97915 | 0.97915 | 0.97961 | |
| Resolution range (Å) | 50.00–1.50 (1.53–1.50) |
50.00–1.30 (1.32–1.30) |
50.00–1.90 (1.93–1.90) |
|
| No. of unique reflections | 43485 (2131) | 79398 (3792) | 11829 (575) | |
| Redundancy | 3.6 (3.5) | 5.9 (5.7) | 3.2 (3.2) | |
| I/σ | 37.9 (2.4) | 39.2 (2.1) | 25.7 (1.9) | |
| Completeness (%) | 99.0 (98.1) | 97.8 (95.1) | 99.1 (100.0) | |
| Rmerge (%)* | 4.7 (62.4) | 5.4 (90.3) | 5.3 (77.1) | |
| Structure refinement | ||||
| Resolution (Å) | 50.0–1.50 (1.55–1.50) |
50.0–1.30 (1.35–1.30) |
50.0–1.90 (1.96–1.90) |
|
| Rcryst†/Rfree‡ | 0.1434 (0.2686)/ 0.1911 (0.3129) |
0.1695 (0.2565)/ 0.1987 (0.2671) |
0.1938 (0.3256)/ 0.2340 (0.3282) |
|
| Rmsd bonds (Å)/angles (°) | 0.009/1.22 | 0.010/1.52 | 0.015/1.67 | |
| Average B factor (Å2)§ | 30.8 | 22.8 | 30.1 | |
| No. of protein atoms | 2046 | 2745 | 1058 | |
| No. of other atoms | 273 | 443 | 96 | |
| No. of reflections | ||||
| Working set | 41244 (4003) | 77272 (7372) | 11252 (1065) | |
| Test set | 2186 (227) | 1947 (190) | 565 (57) | |
| Ramachandran plot (%)§ | ||||
| Favored regions | 99.2 | 99.1 | 98.5 | |
| Allowed regions | 0.8 | 0.9 | 1.5 | |
| Outliers | 0 | 0 | 0 | |
Numbers in parentheses represent the value for the highest resolution shell.
* Rmerge =Σ|Ii - Im|/ΣIi, where Ii is the intensity of the measured reflection and Im is the mean intensity of all symmetry-related reflections.
† Rcryst = Σ||Fobs| - |Fcalc||/Σ|Fobs|, where Fobs and Fcalc are observed and calculated structure factors.
‡ Rfree = ΣT||Fobs| - |Fcalc||/ΣT|Fobs|, where T is a test data set randomly chosen and set aside prior to refinement. For EphA6-Odin, 2.5% of total reflections were enough for the test set during refinement. For EphA2-SHIP2 and EphA5-SAMD5, 5% of total reflections were chosen as test sets.
§ B factors and Ramachandran plot statistics are calculated using MOLPROBITY (Chen et al., 2010).