TABLE 1.
Refinement statistics for the CD1d-GSL-TCR complexes
NA means not available.
| Data collection statistics | CD1d-GCK127-TCR | CD1d-GCK152-TCR | CD1d-NC-αGC-TCR | CD1d-EF77-TCR | CD1d-7DW8–5-TCR |
|---|---|---|---|---|---|
| PDB ID | 4Y4F | 4Y4H | 4Y16 | 4Y4K | 4Y2D |
| Space group | P21 | P21 | C2221 | C2221 | P21 |
| Cell dimension | |||||
| a, b, c (Å) | 78.6, 149.7, 101.4 | 79.4, 150.4, 102.5 | 79.6, 191.9, 151.9 | 79.1, 191.4, 151.3 | 79.4, 150.3, 100.8 |
| α, β, γ (°) | 90, 96.5,90 | 90, 96.4, 90 | 90, 90, 90 | 90, 90, 90 | 90, 96.2, 90 |
| Resolution range (Å) (outer shell) | 40–3.2 (3.31–3.2) | 40–3.1 (3.15–3.1) | 66.21–2.60 (2.71–2.60) | 95.7–2.9 (3.06–2.9) | 500–3.05 (3.12–3.05) |
| No. of reflections | 38,286 | 42,694 | 34,681 | 25,092 | 44,418 |
| Rmerge (%) | 13 (63.9) | 11.3 (59.9) | 10.3 (47.8) | 17.2 (59.4) | 9.3 (53.6) |
| Rpim (%) | NA | NA | 7.0 (32.6) | 11.1 (38.4) | NA |
| Multiplicity | 3.3 (3.3) | 3.8 (4.0) | 2.9 (2.9) | 3.2 (3.4) | 3.0 (3.0) |
| Average I/sI | 13.7 (2.1) | 21.5 (2.7) | 6.8 (2.3) | 5.9 (2.2) | 13.2 (2.0) |
| Completeness (%) | 98.2 (91.1) | 99.4 (100) | 96.2 (95.7) | 97.4 (99.1) | 99.3 (99.8) |
| Refinement statistics | |||||
| No. of atoms | 12,599 | 12,469 | 6,532 | 6,305 | 11,943 |
| Protein | 12,389 | 12,247 | 6,333 | 6,183 | 11,627 |
| Ligand | 126 | 96 | 73 | 56 | 208 |
| Carbohydrate | 84 | 126 | 80 | 66 | 108 |
| Water | 0 | 0 | 46 | 0 | 0 |
| R/Rfree (%) | 21.8/25.7 | 24.2/28.3 | 21.1/24.4 | 21.9/26.5 | 21.7/25.7 |
| Ramachandran plot (%) | |||||
| Favored | 96.91 | 95.52 | 96.36 | 96.11 | 95.93 |
| Allowed | 99.75 | 99.68 | 100 | 99.75 | 99.87 |
| Root mean square deviations | |||||
| Bonds (Å) | 0.006 | 0.01 | 0.01 | 0.005 | 0.005 |
| Angles (°) | 0.879 | 1.226 | 1.248 | 1.076 | 0.994 |
| B-factors (Å2) | |||||
| Protein | 89.25 | 75.42 | 41.75 | 37.58 | 75.66 |
| Ligand | 67.87 | 58.88 | 33.77 | 28 | 50.79 |
| Carbohydrate | 83.86 | 87.85 | 54.56 | 44.54 | 96.54 |