Table 1.
Crystal data, statistics of data collections and statistics of structure refinements
| Bacterial | H. sapiens mitochondrial wild type | H. sapiens mitochondrial A1555G mutant | ||||||
|---|---|---|---|---|---|---|---|---|
| Crystal code | BACT-Co | WT-K | WT-Br-K | MUT-K | MUT-Br1-Sr | MUT-Br1-K1 | MUT-Br1-K2 | MUT-Br2-Co |
| Aminoglycoside | Paromomycin | Paromomycin | Paromomycin | Paromomycin | Paromomycin | Paromomycin | Tobramycin | Paromomycin |
| PDB ID | 3BNL | 3BNN | 3BNO | 3BNP | 3BNQ | 3BNR | 3BNS | 3BNT |
| Crystal data | ||||||||
| Space group | I4 | P1 | P1 | P3121 | C2 | C2 | C2 | P64 |
| Unit cell (Å) (°) | a=b=53.6, c=63.5 | a=34.6, b=44.5, c=52.4 | a=35.2, b=45.5, c=52.2 | a=b=66.6, c=57.6 | a=71.3, b=76.1, c=55.9 | a=71.2, b=77.4, c=56.3 | a=72.7, b=77.1, c=56.5 | a=b=74.9, c=22.5 |
| α=68.8, β=71.3, γ=67.7 | α=71.4, β=73.4, γ=74.0 | β=117.1 | β=115.1 | β=115.7 | ||||
| Za | 1 | 2 | 2 | 1 | 2 | 2 | 2 | 0.5 |
| Data collection | ||||||||
| Beamline | BM30 of ESRF | PX of SLS | ID23-1 of ESRF | PX of SLS | ID23-1 of ESRF* | ID23-1 of ESRF | ID14-2 of ESRF | BM30 of ESRF* |
| Wavelength (Å) | 0.91636 | 0.9999 | 0.8856 | 0.9801 | 0.92070/0.92110/0.91625 | 0.91625 | 0.933 | 0.91950/0.91984/0.91637 |
| Resolution (Å) | 36.8–2.6 | 39.6–2.0 | 29.0–2.35 | 57.7–2.7 | 49.8–2.0/49.8–2.0/49.8–2.0 | 51.0–2.1 | 35.4–1.9 | 37.4–2.3/37.4–2.4/37.4–2.3 |
| Of the outer shell (Å) | 2.7–2.6 | 2.1–2.0 | 2.4-2.35 | 2.9–2.7 | 2.1–2.0/2.1–2.0/2.1–2.0 | 2.2–2.1 | 2.0–1.9 | 2.4–2.3/2.5–2.4/2.4–2.3 |
| Unique reflections | 5295 | 17270 | 11751 | 4263 | 17465/17512/17519 | 16388 | 21598 | 3368/2981/3374 |
| Completeness (%) | 99.9 | 97.0 | 98.0 | 99.4 | 97.4/97.4/97.4 | 99.8 | 97.4 | 100.0/99.9/99.9 |
| In the outer shell (%) | 100.0 | 92.6 | 97.7 | 100.0 | 85.6/85.4/85.5 | 100.0 | 97.4 | 100.0/100.0/100.0 |
| Rmergeb (%) | 5.1 | 9.6 | 9.9 | 7.8 | 4.9/4.9/5.0 | 11.6 | 3.1 | 8.4/9.5/7.2 |
| In the outer shell (%) | 28.6 | 36.9 | 39.0 | 36.4 | 28.0/33.2/37.3 | 37.8 | 37.8 | 30.4/26.9/25.7 |
| Ranomc (%) | – | – | – | – | 5.1/4.0/4.5 | – | – | 6.6/6.5/5.2 |
| In the outer shell (%) | – | – | – | – | 24.6/29.0/33.1 | – | – | 19.0/16.0/15.5 |
| Redundancy | 7.1 | 2.7 | 7.7 | 9.9 | 3.5/3.5/3.5 | 6.9 | 3.8 | 9.9/9.9/9.9 |
| In the outer shell | 7.3 | 2.6 | 8.0 | 10.2 | 2.6/2.6/2.6 | 7.1 | 3.8 | 10.5/10.5/10.5 |
| Structure refinement | ||||||||
| Resolution range (Å) | 36.0–2.6 | 39.6–2.0 | 36.9–2.35 | 40.0–2.7 | 49.8–2.0 | 51.0–2.1 | 35.4–1.9 | 37.4–2.3 |
| Used reflections | 5278 | 17269 | 11718 | 4204 | 17514 | 16147 | 21594 | 3371 |
| R-factord (%) | 22.0 | 23.8 | 22.6 | 23.1 | 22.9 | 21.5 | 24.7 | 21.7 |
| Rfreee | 25.1 | 26.4 | 25.5 | 27.0 | 26.9 | 24.5 | 26.0 | 25.5 |
| Number of DNA atoms | 940 | 1788 | 1788 | 908 | 1942 | 1884 | 1884 | 464 |
| Number of cations | 8 [Co(NH3)6]3+ | – | – | – | 8 Sr2+, 2 K+ | 2 K+ | 2 K+ | 1 [Co(NH3)6]3+, 1 Na+ |
| Number of water | 38 | 114 | 31 | 13 | 191 | 183 | 102 | 55 |
| Number of aminoglycoside | None | None | None | None | 1 (non-specific) | 1 (non-specific) | None | None |
| RMSD | ||||||||
| Bond length (Å) | 0.004 | 0.005 | 0.005 | 0.005 | 0.004 | 0.004 | 0.004 | 0.004 |
| Bond angles (°) | 0.9 | 0.9 | 0.9 | 1.0 | 0.8 | 0.9 | 0.8 | 0.8 |
| Improper angles (°) | 1.3 | 0.7 | 0.7 | 0.9 | 0.7 | 0.7 | 0.7 | 1.3 |
aNumber of dsRNA in the asymmetric unit.
bRmerge=100 × Σhklj|Ihklj – <Ihklj>| / Σhklj < Ihklj>.
cRanom=100 × Σhklj|Ihklj(+) – Ihklj(−)| / Σhklj[Ihklj(+) + Ihklj(−)].
dR-factor=100 × Σ||Fo| – |Fc|| / Σ|Fo|, where |Fo| and |Fc| are optimally scaled observed and calculated structure factor amplitudes, respectively.
eCalculated using a random set containing 10% of observations that were not included throughout refinement (58).
*For phase determination with the multiple anomalous diffraction (MAD) method, three datasets were collected with three wavelengths. Statistics from left to right are of peak, edge and remote data, respectively.