Table 1.
Crystallographic Statistics
| nvSTING–cGG c(G[3′–5′]pG[3′–5′]p) |
nvSTING–3′,3′
cGAMP c(G[3′–5′]pA[3′–5′]p) |
nvSTING–cAA c(A[3′–5′]pA[3′–5′]p) |
nvSTING
Apo “Rotated” |
nvSTING–cGG
(SeMet) c(G[3′–5′]pG[3′–5′]p) |
|
|---|---|---|---|---|---|
| Data Collection | |||||
| Resolution (Å) | 48.54–1.84 (1.90–1.84) | 40.63–1.99 (2.04–1.99) | 40.83–2.95 (3.06–2.95) | 41.15–2.10 (2.16–2.10) | 48.66–2.39 (2.48–2.39) |
| Wavelength (Å) | 1.11587 | 1.11587 | 1.11587 | 1.11587 | 0.97967 |
| Space group | P 31 | P 31 | P 31 | P 31 | P 31 |
| Unit cell: a, b, c (Å) | 81.11, 81.11, 97.07 | 81.27, 81.27, 99.12 | 81.66, 81.66, 98.76 | 82.30, 82.30, 100.35 | 80.77, 80.77, 97.33 |
| Unit cell: α, β, γ (°) | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 |
| Molecules per ASU | 2 | 2 | 2 | 2 | 2 |
| No. reflections: total | 693819 | 473676 | 89635 | 494252 | 323356 |
| No. reflections: unique | 61587 | 49839 | 15258 | 43684 | 27919 |
| Completeness (%) | 98.7 (82.5) | 99.5 (93.9) | 98.3 (85.5) | 98.4 (81.1) | 99.2 (92.7) |
| Multiplicity | 11.3 (9.3) | 9.5 (8.2) | 5.8 (5.5) | 11.3 (8.1) | 11.6 (10.9) |
| I/σI | 10.3 (1.5) | 13.4 (1.8) | 6.1 (1.0) | 9.4 (1.0) | 17.1 (5.2) |
| CC(1/2) (%) | 99.8 (50.8) | 99.9 (63.4) | 95.9 (34.4) | 99.8 (34.0) | 99.8 (91.5) |
| Rpim (%) | 3.6 (69.9) | 3.3 (73.9) | 10.5 (89.2) | 4.4 (88.2) | 3.7 (16.2) |
| No. sites | 8 | ||||
| Refinement | |||||
| Resolution (Å) | 48.54–1.84 | 40.63–1.99 | 40.83–2.95 | 41.15–2.10 | |
| Free reflections (%) | 5 | 5 | 5 | 5 | |
| R-factor / R-free | 17.2 / 20.9 | 16.9 / 19.0 | 22.1 / 24.6 | 17.2 / 20.2 | |
| Bond distance (RMS Å) | 0.003 | 0.008 | 0.003 | 0.011 | |
| Bond angles (RMS °) | 0.740 | 1.053 | 0.944 | 1.322 | |
| Structure/Stereochemistry | |||||
| No. atoms: protein | 3060 | 3060 | 3063 | 3006 | |
| No. atoms: ligand | 46 | 45 | 88 | 0 | |
| No. atoms: water | 392 | 256 | 0 | 209 | |
| Average B-factor: protein | 37.6 | 51.3 | 74.4 | 54.2 | |
| Average B-factor: ligand | 24.7 | 33.5 | 85.9 | - | |
| Average B-factor: solvent | 47.6 | 52.7 | - | 55.8 | |
| Ramachandran plot: favored | 98.4% | 97.8% | 98.6% | 97.8 | |
| Ramachandran plot: allowed | 1.6% | 2.2% | 1.4% | 2.2 | |
| Ramachandran plot: outliers | 0% | 0% | 0% | 0% | |
| Rotamer outliers: | 0.9% | 0.9% | 1.5% | 1.2% | |
| MolProbity score | 1.06 | 1.29 | 1.49 | 1.19 | |
| Protein Data Bank ID | 5CFL | 5CFM | 5CFN | 5CFO | |
| nvSTING–cGG
F276K c(G[3′–5′]pG[3′–5′]p) |
nvSTING–2′,3′
cGAMP c(G[2′–5′]pA[3′–5′]p) |
nvSTING
Apo “Unrotated” |
|
|---|---|---|---|
| Data Collection | |||
| Resolution (Å) | 40.93–2.07 (2.12–2.07) | 42.49–2.10 (2.16–2.10) | 43.04–2.85 (3.00–2.85) |
| Wavelength (Å) | 1.11588 | 1.11587 | 1.11587 |
| Space group | P 31 | P 21 21 21 | P 21 21 21 |
| Unit cell: a, b, c (Å) | 81.39, 81.39, 100.55 | 40.50, 77.97, 101.35 | 43.04, 43.04, 170.94 |
| Unit cell: α, β, γ (°) | 90.0, 90.0, 120.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Molecules per ASU | 2 | 2 | 2 |
| No. reflections: total | 290406 | 283149 | 31005 |
| No. reflections: unique | 45536 | 19434 | 7901 |
| Completeness (%) | 99.6 (94.6) | 99.6 (95.6) | 99.4 (97.5) |
| Multiplicity | 6.4 (6.0) | 14.6 (6.6) | 3.9 (4.0) |
| I/σI | 8.0 (1.1) | 16.2 (1.6) | 12.6 (3.2) |
| CC(1/2) (%) | 99.5 (31.3) | 99.9 (62.1) | 99.7 (97.5) |
| Rpim (%) | 5.2 (90.1) | 2.4 (54.1) | 3.8 (23.1) |
| Refinement | |||
| Resolution (Å) | 40.93–2.07 | 42.49–2.10 | 43.04–2.85 |
| Free reflections (%) | 5 | 5 | 5 |
| R-factor / R-free | 17.2 / 20.6 | 24.2 / 25.9 | 25.7 / 27.8 |
| Bond distance (RMS Å) | 0.009 | 0.003 | 0.003 |
| Bond angles (RMS °) | 1.298 | 0.733 | 0.805 |
| Structure/Stereochemistry | |||
| No. atoms: protein | 2986 | 2963 | 2844 |
| No. atoms: ligand/ion | 92 | 45 | 4 (Calcium) |
| No. atoms: water | 241 | 56 | 3 |
| Average B-factor: protein | 48.7 | 67.4 | 64.7 |
| Average B-factor: ligand/ion | 54.4 | 31.1 | 76.5 |
| Average B-factor: water | 53.5 | 51.1 | 14.2 |
| Ramachandran plot: favored | 98.0% | 96.1% | 94.6% |
| Ramachandran plot: allowed | 2.0% | 3.9% | 5.4% |
| Ramachandran plot: outliers | 0% | 0% | 0% |
| Rotamer outliers: | 1.2% | 0.6% | 4.8% |
| MolProbity score | 1.35 | 1.72 | 2.28 |
| Protein Data Bank ID | 5CFP | 5CFQ | 5CFR |