Table 2.
X-ray diffraction data collection and refinement statistics
| TDP1–Compound 1 (cocktail soak) | TDP1–Compound 1 (single soak) | TDP1–Compound 2 (cocktail soak) | TDP1–Compoiund 2 (single soak) | TDP1–Compound 3 | TDP1–Compound 4 | TDP1–Compound 5 | TDP1–Compound 6 | TDP1–Compound 7 | TDP1–Compound 8 | TDP1–Compound 9 | TDP1–Compound 10 | TDP1–Compound 11 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fragment concentration (mM) | 5 | 20 | 5 | 20 | 20 | 5.5 | 17 | 20 | 22.5 | 4.5 | 13.6 | 9.9 | 16.4 |
| Diffraction Source | SER-CAT 22-ID | SER-CAT 22-BM | SER-CAT 22-BM | SER-CAT 22-BM | SER-CAT 22-ID | SER-CAT 22-BM | SER-CAT 22-BM | SER-CAT 22-ID | SER-CAT 22-ID | SER-CAT 22-ID | SER-CAT 22-ID | SER-CAT | SER-CAT |
| Wavelength (Å) | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.00000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 |
| a-, b = , c = (Å) | 50.05, 105.26, 193.91 | 50.09, 105.63, 194.03 | 50.11, 105.64, 194.95 | 50.12, 105.41, 194.56 | 49.91, 105.59, 194.19 | 49.77, 104.99, 194.11 | 49.94, 105.14, 193.37 | 50.06, 105.37, 194.58 | 50.16, 105.31, 193.98 | 50.07, 105.14, 194.45 | 50.16, 105.59, 193.98 | 50.05, 105.41, 194.1 | 49.96, 105.06, 193.32 |
| α=,β=,γ= (°) | 90,90,90 | 90, 90, 90 | 90, 90, 90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 | 90,90,90 |
| Data Collection Statistics | |||||||||||||
| Resolution Range (Å) | 50–1.63 (1.66–1.63)a | 50–1.78 (1.81-1.78) | 50-1.81 (1.84–1.81) | 50–1.78 (1.81–1.78) | 50–1.78 (1.81–1.78) | 50–1.75 (1.78–1.75) | 5–1.74 (1.77–1.74) | 50–1.70 (1.73–1.70) | 50–1.67 (1.70–1.67) | 50–1.91 (1.94–1.91)a | 50–1.85 (1.88–1.85) | 50–1.62 (1.65–1.62) | 50–1.50 (1.53–1.50) |
| Total No. of reflection | 876 873 | 632 682 | 395 972 | 492 373 | 1 443 515 | 630 560 | 536 200 | 781 610 | 841 105 | 531 475 | 544 340 | 908 312 | 1 022 403 |
| Total No. of unique reflections | 128 455 | 99 895 | 93 819 | 98 896 | 100 750 | 105 159 | 105 222 | 112 529 | 120 178 | 78 029 | 83 875 | 131 858 | 157 054 |
| Completeness (%) | 99.6 (98.4) | 100 (100) | 97.8 (98.5) | 98.7 (98.2) | 99.9 (100) | 99.6 (94.3) | 99.9 (97.8) | 99.7 (98.7) | 99.6 (99.3) | 98.3 (96.5) | 95.0 (93.8) | 100 (99.8) | 96.2 (92.9) |
| CC1/2b | 0.754 | 0.769 | 0.622 | 0.733 | 0.891 | 0.925 | 0.956 | 0.790 | 0.870 | 0.754 | 0.817 | 0.760 | 0.802 |
| Multiplicity | 6.8 (6.1) | 6.3 (6.1) | 4.2 (3.8) | 5.0 (4.9) | 14.3 (14.0) | 6.0 (5.1) | 5.1 (4.4) | 6.9 (5.7) | 7.0 (6.5) | 6.8 (6.6) | 6.5 (6.0) | 6.9 (6.1) | 6.5 (5.7) |
| I/(σ) I | 38.2 (2.3) | 32.7 (3.1) | 29.2 (2.3) | 29.3 (2.3) | 48.3 (4.5) | 41.7 (4.9) | 39.8 (6.7) | 35.4 (3.0) | 37.8 (3.5) | 28.4 (2.6) | 25.7 (2.5) | 28.1 (2.2) | 37.2 (2.0) |
| Rsym | 0.062 (0.711) | 0.078 (0.918) | 0.071 (0.882) | 0.071 (0.561) | 0.117 (0.780) | 0.051 (0.327) | 0.050 (0.215) | 0.081 (0.811) | 0.072 (0.771) | 0.088 (0.957) | 0.104 (0.801) | 0.071 (0.046) | 0.046 (0.806) |
| Rpim | 0.025 (0.311) | 0.034 (0.405) | 0.036 (0.501) | 0.035 (0.289) | 0.032 (0.219) | 0.023 (0.157) | 0.024 (0.115) | 0.033 (0.352) | 0.030 (0.316) | 0.036 (0.343) | 0.043 (0.342 | 0.027 (0.349) | 0.023 (0.353) |
| Refinement Statistics | |||||||||||||
| Resolution Range (Å) | 35.66–1.63 | 37.08–1.78 | 40.99–1.81 | 37.12–1.78 | 40.91–1.77 | 36.12–1.75 | 36.96–1.74 | 35.68–1.70 | 35.70–1.67 | 37.08–1.91 | 36.42–1.85 | 35.7–1,62 | 36.3–1.50 |
| Final Rwork | 0.181 | 0.179 | 0.186 | 0.186 | 0.179 | 0.181 | 0.174 | 0.191 | 0.188 | 0.178 | 0.178 | 0.180 | 0.180 |
| Final Rfree | 0.211 | 0.215 | 0.227 | 0.227 | 0.216 | 0.211 | 0.206 | 0.227 | 0.212 | 0.228 | 0.218 | 0.202 | 0.201 |
| No. of non H-atoms/Average B factor (Å2) | |||||||||||||
| Protein chain A | 3640/38.5 | 3599/26.1 | 3605/28.6 | 3612/25.7 | 3627/24.8 | 3633/22.7 | 3625/19.0 | 3609/24.7 | 3616/23.9 | 3616/26.5 | 3626/23.7 | 3623/23.7 | 3654/24.8 |
| Protein chain B | 3619/30.3 | 3601/31.5 | 3610/34.9 | 3582/32.1 | 3596/29.1 | 3619/25.9 | 3621/23.0 | 3587/32.0 | 3616/30.2 | 3601/33.9 | 3591/30.6 | 3618/28.3 | 3606/28.5 |
| Water | 695/38.9 | 676/38.7 | 582/39.5 | 727/38.8 | 711/38.2 | 779/34.7 | 886/33.4 | 648/38.6 | 619/37.6 | 586/38.9 | 580/36.9 | 842/38.9 | 796/40.0 |
| Ligand chain A | 15/37.2 | 15/29.8 | 14/36.3 | 14/32.7 | 13/28.6 | 13/26.5 | 13/20.0 | 17/31.5 | 17/38.2 | 15/37.2 | 17/36.4 | 20/29.7 | 21/33.5 |
| Ligand chain B | 15/39.5 | 15/35.1 | 14/45.3 | 14/44.0 | 13/30.8 | 13/26.4 | 13/21.7 | 17/36.2 | 17/39.1 | 15/37.2 | 17/39.3 | 20/34.5 | 17/31.1 |
| Ethylene glycol | 40/37.9 | 16/31.7 | 24/37.7 | 16/29.5 | 12/26.0 | 24/28.6 | 28/27.6 | 16/30.6 | 16/30.8 | 12/29.9 | 12/32.5 | 20/32.6 | 12/30.4 |
| R.m.s.d from ideal | |||||||||||||
| Bond lengths (Å) | 0.006 | 0.006 | 0.007 | 0.007 | 0.006 | 0.006 | 0.006 | 0.006 | 0.006 | 0.007 | 0.006 | 0.006 | 0.005 |
| Bond angles (°) | 0.8 | 0.8 | 0.8 | 0.8 | 0.8 | 0.8 | 0.8 | 0.8 | 0.8 | 0.9 | 0.8 | 0.8 | 0.8 |
| Ramachandran plot | |||||||||||||
| Favored (%) | 98.3 | 98.0 | 97.7 | 97.1 | 98.2 | 97.9 | 97.9 | 97.6 | 97.6 | 97.6 | 97.9 | 97.8 | 98.0 |
| Allowed (%) | 1.6 | 1.9 | 2.0 | 2.6 | 1.7 | 2.0 | 2.0 | 2.3 | 2.1 | 2.3 | 1.9 | 1.9 | 1.9 |
| Disallowed (%) | 0.1 | 0.1 | 0.3 | 0.3 | 0.1 | 0.1 | 0.1 | 0.1 | 0.3 | 0.1 | 0.2 | 0.3 | 0.1 |
| Molprobity score | 1.08 (99th percentile) | 0.98 (100th percentile) | 1.06 (100th percentile) | 1.17 (99th percentile) | 1.05 (100th percentile) | 1.12 (99th perecentile) | 1.06 (100th percentile) | 1.24 (98th percentile) | 1.19 (99th percentile) | 1.23 (99th percentile | 2.09 (100th percentile) | 3.7 (97th percentile) | 2.5 (99th percentile) |
| PDB code: | 6DHU | 6DIE | 6DIM | 6DJD | 6DIH | 6DJI | 6DJJ | 6DJE | 6DJF | 6DJH | 6MJ5 | 6N17 | 6N19 |
aValues in parenthesis are for the highest-resolution shell of data.
bValue is for the highest-resolution shell of data.