Table 1. Summary of Statistics of X-ray diffraction and refinement*.
| Protein | NgTet1Δ57 | |
|---|---|---|
| DNA | 5′-TGGAAHGCAATTCT-3′ | 5′-TGTCAGMGCATGG-3′ |
| (M = 5mC; H = 5hmC) | 3′-ACCTTGCGTTAAGA-5′ | 3′-CAGTCGCGTACCT-5′ |
| Cofactor / Metal | αKG/Mn(II) | αKG/Mn(II) |
| PDB | 5CG8 | 5CG9 |
| Beamline/wavelength | SER-CAT 22-BM/1.0 Å | SER-CAT 22-ID/1.0 Å |
| Space group | I212121 | P3221 |
| Unit cell (a, b, c (Å)) | 83.8, 107.4, 167.7 | 191.2, 191.2, 51.3 |
| (α, β, γ (°)) | 90, 90, 90 | 90, 90, 120 |
| Resolution (Å) | 27.6–2.69 (2.79–2.69) | 29.7–2.69 (2.79–2.69) |
| aRmerge | 0.066 (0.977) | 0.154 (0.894) |
| b <I/σI> | 29.2 (2.9) | 13.7 (2.2) |
| Completeness (%) | 99.7 (100.0) | 98.7 (92.8) |
| Redundancy | 9.9 (10.0) | 9.3 (8.9) |
| CC 1/2, CC | (0.908/0.976) | (0.796/0.942) |
| Reflections (observed) | 208 582 | 274 840 |
| (Unique) | 20 985 | 29 462 |
| Refinement | (1 complex in asymmetric unit) | (Two complexes in asymmetric unit) |
| Resolution (Å) | 2.70 | 2.69 |
| No. of reflections | 20 958 | 29 452 |
| cRwork/dRfree | 0.189/0.228 | 0.217/0.238 |
| No. of atoms | ||
| Protein | 2094 | 4211 |
| DNA | 570 | 953 |
| αKG | 10 | 20 |
| Mn(II) | 1 | 2 |
| Solvent | 11 | 42 |
| B-factors (Å2) | ||
| Protein | 86.2 | 70.9 |
| DNA | 111.1 | 98.8 |
| αKG | 80.5 | 69.6 |
| Mn(II) | 65.9 | 68.2 |
| Solvent | 97.5 | 73.7 |
| R.M.S. deviations | ||
| Bond length (Å) | 0.008 | 0.006 |
| Bond angles (°) | 1.0 | 0.8 |
| All atom clash score | 0.8 | 2.1 |
| Ramachandran plot (%) | ||
| Favored | 98.5 | 99.0 |
| Allowed | 1.5 | 1.0 |
| Rotamer outliers (%) | 0 | 0.2 |
| Cβ deviation | 0 | 0 |
*Values in parenthesis correspond to highest resolution shell.
aRmerge = Σ|I – <I>| /ΣI, where I is the observed intensity and <I> is the averaged intensity from multiple observations.
b <I/σI> = averaged ratio of the intensity (I) to the error of the intensity (σI).
cRwork = Σ|Fobs – Fcal |/Σ| Fobs |, where Fobs and Fcal are the observed and calculated structure factors, respectively.
dRfree was calculated using a randomly chosen subset (5%) of the reflections not used in refinement.