TABLE 1.
Data collection and refinement statistics
| CNTN3(Ig2-Ig3)·PTPRG(CA) | CNTN6(Ig2-Ig3)·PTPRG(CA) | CNTN5(Ig1–Ig4) | CNTN1 (FN1–FN3) | SeCNTN2 (FN1–FN3) | CNTN2 (FN1–FN3) | CNTN3 (FN1-FN3) | CNTN3 (Ig5-FN2) | CNTN4 (FN1–FN3) | CNTN5 (FN1–FN3) | CNTN6 (FN1–FN3) | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Data collection | |||||||||||
| Beamline | APS 22-ID | APS 22-BM | APS 22-BM | APS 22-ID | APS 22-BM | APS 22-ID | APS 22-ID | APS 22-BM | APS 22-BM | APS 22-ID | APS 22-ID |
| Wavelength (Å) | 1.0 | 1.0 | 1.0 | 1.0 | 0.97916 | 1.0 | 1.0 | 1.0 | 0.97933 | 1.0 | 1.0 |
| Unique reflections | 31,166 | 70,482 | 14,070 | 48,701 | 49,121 | 28,357 | 8,976 | 20,578 | 13,387 | 14,285 | 21,656 |
| Resolution (Å) | 50–2.6 | 50–2.0 | 50–2.6 | 50–2.5 | 50–1.8 | 30–2.0 | 50–2.8 | 50–2.4 | 50–2.5 | 50–2.7 | 50–2.7 |
| Space group | P21212 | P212121 | C2 | P21 | P21212 | P21212 | C2 | P212121 | C2221 | C2221 | P212121 |
| Unit cell | |||||||||||
| a, b, c (Å) | 74.14, 90.53, 147.45 | 78.64, 113.53, 117.05 | 179.98, 50.66, 51.02 | 87.48, 49.87, 163.30 | 124.82, 40.85, 83.11 | 124.39, 40.67, 82.60 | 185.10, 39.03, 52.40 | 58.22, 76.93, 115.82 | 94.79, 144.3, 55.40 | 83.77, 154.52, 90.42 | 86.74, 90.85, 99.35 |
| α, β, γ (degrees) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 101.67, 90.0 | 90.0, 97.12, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 96.9, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Rsyma | 0.134 (0.588)b | 0.096 (0.593) | 0.154 (0.435) | 0.075 (0.380) | 0.082 (0.479) | 0.110 (0.508) | 0.139 (0.377) | 0.165 (0.548) | 0.08 (0.460) | 0.112 (0.418) | 0.155 (0.515) |
| Completenessb (%) | 99.6 (96.3) | 98.7 (89.2) | 98.8 (90.7) | 99.2 (92.3) | 99.1 (92.7) | 97.8 (89.3) | 97.7 (90.0) | 98.2 (87.5) | 98.3 (87.4) | 85.7 (56.3) | 97.9 (92.5) |
| Redundancy | 11.4 (5.3) | 7.1 (5.3) | 6.5 (3.5) | 6.9 (4.7) | 7.0 (5.6) | 5.9 (3.2) | 8.9 (5.8) | 11.9 (7.9) | 6.1 (4.2) | 12 (5.9) | 7.4 (4.8) |
| I/iΣi | 7.2 (2.3) | 19.5 (2.0) | 11.4 (2.3) | 20.4 (3.3) | 19.8 (2.7) | 12.5 (1.6) | 15.0 (4) | 14.8 (2.4) | 20.7 (2.3) | 17.35 (3.6) | 8.4 (2.1) |
| Refinement | |||||||||||
| Molecules in asymmetric unit | 2 × 2 | 2 × 2 | 1 | 4 | 1 | 1 | 1 | 1 | 1 | 2 | |
| Resolution (Å) | 49.2–2.6 | 24.9–2.0 | 37.0–2.6 | 43.5–2.5 | 29.1–2.0 | 47.8–2.8 | 43.1–2.4 | 28.7–2.5 | 38.6–2.7 | 43.4–2.7 | |
| Rworkc/Rfree | 0.187/0.249 | 0.167/0.217 | 0.195/0.264 | 0.204/0.247 | 0.190/0.226 | 0.183/0.244 | 0.203/0.253 | 0.190/0.255 | 0.194/0.231 | 0.200/241 | |
| No. of atoms | 7,291 | 8,039 | 3,086 | 9,572 | 2,491 | 2,135 | 3,190 | 2,394 | 2,282 | 4,715 | |
| Protein | 7,205 | 7,392 | 2,968 | 9,267 | 2,301 | 2,110 | 3,032 | 2,325 | 2,258 | 4,672 | |
| Ligand | 27 | 112 | 28 | 75 | 6 | 5 | |||||
| Water | 59 | 535 | 90 | 230 | 190 | 25 | 152 | 69 | 19 | 43 | |
| Root mean square deviations | |||||||||||
| Ideal bonds (Å) | 0.009 | 0.007 | 0.003 | 0.004 | 0.007 | 0.01 | 0.009 | 0.009 | 0.009 | 0.004 | |
| Ideal angles (degrees) | 1.10 | 1.05 | 0.83 | 0.84 | 1.06 | 1.21 | 1.28 | 1.12 | 1.13 | 0.92 | |
| Average B factors (Å2) | 71.2 | 40.9 | 50.1 | 63.7 | 39.2 | 57 | 41.2 | 61.6 | 93.7 | 42.8 | |
| Protein | 71.3 | 40.4 | 49.6 | 63.9 | 39.1 | 57.2 | 41.3 | 61.8 | 93.8 | 42.9 | |
| Ligand | 98.3 | 71.9 | 88.0 | 85.5 | 62.9 | 121.1 | |||||
| Water | 49.9 | 41.6 | 51.6 | 50.2 | 40.5 | 38.9 | 36.9 | 53.5 | 69.7 | 34.9 | |
| Ramachandran statistics | |||||||||||
| Favored (%) | 94 | 97 | 95 | 96 | 98 | 95 | 96 | 97 | 94 | 97 | |
| Allowed (%) | 6 | 3 | 5 | 4 | 2 | 5 | 4 | 3 | 6 | 3 | |
| PDB accession code | 5E5R | 5E5U | 5E4I | 5E53 | 5E7L | 5E4Q | 5I99 | 5E4S | 5E52 | 5E55 | |
a Rsym = Σh Σi|Ii(h) − 〈I(h)〉|/Σh Σi Ii(h), where Ii(h) is the ith measurement of reflection h and 〈I(h)〉 is a weighted mean of all measurements of h.
b Values in parentheses apply to the high resolution shell.
c r = Σh Fo(h) − Fc(h)|/Σh|Fo|. Rwork and Rfree were calculated from the working and test reflection sets, respectively.