Table 1.
Data collection and refinement statistics.
| Apo NPP3 | NPP3xAMP | NPP3T206AxAMPNPP | NPP3T206AxAp4A | NPP3T206AxUDPGlcNAc | |
|---|---|---|---|---|---|
| PDB code | 6F2T | 6F2V | 6F33 | 6F2Y | 6F30 |
| Data collection | |||||
| Beamline | BESSY MX 14.1 | BESSY MX 14.1 | BESSY MX 14.1 | BESSY MX 14.1 | BESSY MX 14.1 |
| Wavelength (Å) | 0.91843 | 0.91842 | 0.91841 | 0.91842 | 0.91800 |
| Space group | P21 | P21 | P21 | P21 | P21 |
| Cell dimensions | |||||
| a, b, c (Å) | 73.8, 124.1, 110.7 | 74.2, 125.3, 112.2 | 74.5, 126.9, 112.2 | 75.0, 126.8, 114.5 | 75.3, 127.7, 113.4 |
| α, β, γ (°) | 90, 97.0, 90 | 90, 97.0, 90 | 90, 96.8, 90 | 90, 97.5, 90 | 90, 97.1, 90 |
| Resolution range (Å) | 47.3–2.4 (2.45–2.4) | 37.8–2.5 (2.54–2.5) | 47.3–2.9 (2.95–2.9) | 48.2–2.4 (2.45–2.4) | 37.5–2.3 (2.34–2.3) |
| Completeness (%) | 99.5 (100) | 99.8 (99.8) | 98.2 (98.7) | 98.9 (99.8) | 99.7 (99.9) |
| Multiplicity | 3.4 (4.0) | 3.6 (3.6) | 2.8 (2.8) | 3.0 (3.1) | 3.4 (3.5) |
| 〈I/σ(I)〉 | 7.6 (1.0) | 12.3 (2.0) | 2.4 (1.4) | 7.8 (1.4) | 9.9 (1.2) |
| Rr.i.m.(%) | 13.1 (124.8) | 9.7 (74.5) | 23.7 (64.5) | 12.2 (102.9) | 8.7 (126.1) |
| CC1/2 | 99.5 (62.3) | 99.7 (68.4) | 95.7 (60.7) | 99.5 (53.2) | 99.8 (59.6) |
| Overal B factor from Wilson plot (Å2) | 43.8 | 38.0 | 51.8 | 40.4 | 43.2 |
| No. of Reflections | 76975 | 70943 | 40761 | 81943 | 94004 |
| Refinement | |||||
| Resolution range (Å) | 47.4–2.4 | 37.8–2.5 | 47.3–2.9 | 48.2–2.4 | 37.5–2.3 |
| Rwork/Rfree (%) | 21.5/22.9 | 19.4/20.9 | 24.5/26.8 | 20.4/21.7 | 19.6/21.3 |
| No. of Atoms | |||||
| Protein | 11524 | 11612 | 11597 | 11583 | 11610 |
| Water | 474 | 464 | 0 | 431 | 611 |
| Glycans, Ligands, Ions | 234 | 273 | 250 | 367 | 333 |
| Average B-factors (Å2) | |||||
| Protein | 55.6 | 50.0 | 68.2 | 53.6 | 56.4 |
| Water | 46.8 | 40.0 | — | 43.7 | 49.5 |
| Ligands | 70.0 | 62.7 | 73.9 | 71.5 | 75.4 |
| R. m. s. deviation | |||||
| Bond length (Å) | 0.007 | 0.007 | 0.007 | 0.007 | 0.007 |
| Bond angles (°) | 0.96 | 0.94 | 0.88 | 0.91 | 0.94 |
| Ramachandran plot | |||||
| Favored region (%) | 96.2 | 95.4 | 92.7 | 96.2 | 95.3 |
| Allowed region (%) | 3.6 | 4.5 | 7.1 | 3.6 | 4.5 |
| Outlier region (%) | 0.2 | 0.1 | 0.2 | 0.2 | 0.1 |