TABLE 1.
Data collection and refinement statistics (values in parentheses refer to the highest resolution shell)
| TgNTPDase3 apo | TgNTPDase3 thiomerosal | TgNTPDase3 KI | TgNTPDase3 cis-Pt(NH3)2Cl2 | TgNTPDase3−AMP | TgNTPDase3ΔCC ×Mg2+−AMPPNP | TgNTPDase1ΔCC | |
|---|---|---|---|---|---|---|---|
| Data collection | |||||||
| X-ray source | BL14.1/HZB | BL14.1/HZB | BL14.1/HZB | BL14.1/HZB | BL14.1/HZB | BL14.2/HZB | ID23–2/ESRF |
| Wavelength (Å) | 0.91841 | 0.83 | 1.9 | 0.89 | 0.91841 | 0.91841 | 0.8726 |
| Space group | P21 | P21 | P21 | P21 | P21 | C2221 | C2221 |
| Cell dimensions | |||||||
| a (Å) | 89.0 | 88.9 | 89.4 | 88.9 | 89.2 | 72.0 | 73.7 |
| b (Å) | 165.9 | 164.4 | 165.8 | 164.7 | 166.0 | 150.8 | 150.4 |
| c (Å) | 97.5 | 97.6 | 97.3 | 97.3 | 97.9 | 487.1 | 242.4 |
| β (degrees) | 97.0 | 97.1 | 97.4 | 97.1 | 97.2 | 90 | 90 |
| Wilson B factor (Å2) | 21.5 | 55.5 | 72.8 | 51.3 | 33.0 | 49.6 | 42.1 |
| Resolution (Å) | 40.39–2.00 | 54.00–2.90 | 55.22–3.20 | 60.19–2.90 | 43.40–2.20 | 39.00–2.85 | 39.30–2.60 |
| Resolution, last shell (Å) | 2.11–2.00 | 3.06–2.90 | 3.37–3.20 | 3.06–2.90 | 2.30–2.20 | 3.00–2.85 | 2.60–2.50 |
| Unique reflections | 183,360 | 61,578 | 46,364 | 61,544 | 142618 | 61587 | 47598 |
| Average multiplicity | 5.1 (5.0) | 5.1 (5.1) | 5.3 (5.2) | 4.7 (4.6) | 3.0 (2.9) | 3.7 (3.4) | 4.4 (3.9) |
| Completeness (%) | 97.3 (97.9) | 99.9 (99.9) | 100 (100) | 100 (100) | 96.9 (93.3) | 98.3 (94.3) | 99.9 (99.6) |
| 〈I/σI〉 | 10.1 (2.9) | 8.2 (2.9) | 9.3 (3.3) | 8.3 (2.8) | 7.6 (2.0) | 5.0 (2.0) | 11.9 (3.0) |
| Rmerge (%)a | 10.5 (50.8) | 12.9 (43.1) | 13.2 (46.9) | 12.9 (44.6) | 8.1 (48.9) | 16.9 (45.2) | 9.6 (47.4) |
| Rrim (%)a | 11.7 (56.6) | 16.4 (54.7) | 16.9 (59.0) | 16.7 (57.0) | 11.5 (68.9) | 22.7 (60.4) | 10.9 (55.5) |
| Rpim (%)a | 5.0 (24.5) | 7.2 (23.9) | 7.3 (25.8) | 7.7 (26.4) | 6.4 (40.0) | 15.1 (39.7) | 5.1 (27.7) |
| Refinement | |||||||
| Resolution range (Å) | 40.39–2.00 | 43.40–2.20 | 39.00–2.85 | 39.30–2.50 | |||
| Rwork/Rfree (%) | 17.4/20.9 | 18.0/22.8 | 23.4/28.4 | 17.6/22.6 | |||
| No. of amino acids | 2369 | 2371 | 2360 | 1185 | |||
| Water | 1274 | 884 | 0 | 247 | |||
| Ligandsb | 4 | 5 | 8 | 0 | |||
| Average B factor (Å2) | |||||||
| Protein | 31.9 | 41.6 | 20.4 | 36.5 | |||
| Water | 33.8 | 37.2 | 30.8 | ||||
| Ligandsb | 33.0 | 46.8 | 59.4 | ||||
| rmsd bond length (Å)c | 0.009 | 0.010 | 0.010 | 0.010 | |||
| rmsd angles (degrees)c | 1.03 | 1.14 | 1.45 | 1.19 | |||
| Ramachandran plots | |||||||
| Favored (%) | 98.7 | 98.8 | 97.1 | 98.5 | |||
| Allowed (%) | 100 | 99.9 | 100 | 100 | |||
| No. of outliers | 1 | 2 | 0 | 0 | |||
| Protein Data Bank accession code | 4a57 | 4a59 | 4a5a | 4a5b | |||