Table 1 Data collection and refinement statistics for brachyury DNA complexes and ground state models
Brachyury + DNA | Brachyury D177 + DNA | Brachyury + ssDNA | Brachyury WT ground state | Brachyury D177 ground state | |
|---|---|---|---|---|---|
Space group | P 21 | P 43 2 2 | P 61 2 2 | P 41 2 2 | H 3 2 |
Cell dimensions, a,b,c (Å) | 75.0, 37.1, 110.8 | 75.3, 75.3, 288.5 | 63.0, 63.0, 218.5 | 60.3, 60.3, 110.0 | 99.7, 99.7, 99.3 |
Wavelength (Å) | 0.92 | 0.92 | 0.97 | 0.92 | 0.92 |
Resolution (Å) | 29.6–2.25 (2.33–2.25) | 72.0–2.15 (2.21–2.15) | 109–2.55 (2.62–2.55) | 52.9–1.54 (1.59–1.54) | 49.8–1.42 (1.45–1.42) |
Rmerge | 0.123 (0.689) | 0.113 (2.560) | 0.109 (2.810) | 0.092 (2.0) | 0.038 (1.198) |
I/σI | 6.1 (1.5) | 12.9 (1.2) | 15.9 (1.0) | 12.3 (1.2) | 21 (1.2) |
CC1/2 | 0.992 (0.653) | 0.997 (0.777) | 1.00 (0.593) | 0.998 (0.645) | 1.0 (0.562) |
Completeness % | 97.6 (94.1) | 99.9 (98.7) | 100 (100) | 99.8 (100) | 100 (100) |
Multiplicity | 3.4 (3.4) | 25.5 (23.1) | 17.4 (15.7) | 12.1 (10) | 8.2 (8.0) |
No. unique reflections | 27866 (2466) | 46387 (3687) | 9158 (666) | 30913 (2746) | 35889 (2607) |
Refinement statistics | |||||
Resolution | 29.6–2.25 | 72.0–2.15 | 109–2.55 | 52.9–1.54 | 49.8–1.42 |
Rwork/Rfree (%) | 22.56/28.82 | 22.14/25.20 | 27.33/30.18 | 22.64/24.11 | 19.75/22.31 |
No. atoms | 4131 | 4105 | 1937 | 1462 | 1612 |
Protein | 2843 | 2924 | 1449 | 1382 | 1425 |
Solvent | 335 | 112 | 2 | 75 | 186 |
DNA | 952 | 1060 | 486 | 0 | 0 |
Average B factors (Å2) | |||||
All atoms | 38 | 69 | 82 | 36 | 25 |
Protein | 37 | 70 | 82 | 35 | 24 |
Solvent | 42 | 61 | 62 | 34 | 25 |
DNA | 30 | 65 | 82 | – | – |
Wilson B | 34 | 59 | 71 | 25.4 | 21.5 |
R.M.S. deviations | |||||
Bond lengths (Å) | 0.007 | 0.008 | 0.006 | 0.008 | 0.012 |
Bond angles (°) | 0.90 | 0.96 | 1.055 | 0.98 | 1.45 |
Ramachandran plot | |||||
Favored (%) | 99 | 99 | 92 | 95 | 97 |
Allowed (%) | 1 | 1 | 7 | 3 | 3 |
PDB ID | 6F58 | 6F59 | 8CDN | 7HI8 | 7HI9 |
