TABLE 3.
X-ray diffraction data and model refinement statistics
| Parameter | Data for: |
|
|---|---|---|
| RT3MB/M184V-DNA-dGTP | RT3MB/M184V/F160M-DNA-dCTP | |
| Data collection | ||
| Beamline | PF BL-1A | PF BL-1A |
| Wavelength (Å) | 1.1000 | 1.1000 |
| Temperature (K) | 100 | 100 |
| Detector | Eiger X4M | Eiger X4M |
| Space group | H3 | H3 |
| Unit cell parameters (Å) | a = b = 283.5, c = 96.1 | a = b = 285.7, c = 96.3 |
| Resolution (Å)a | 50–2.43 (2.47–2.43) | 50–2.67 (2.83–2.67) |
| No. of unique reflections | 107,363 | 83,121 |
| Rmeasa,b | 0.103 (0.819) | 0.089 (0.982) |
| Mean I/σ (I)a | 10.5 (2.1) | 14.8 (2.0) |
| Completeness (%)a | 100.0 (100.0) | 100.0 (99.6) |
| Multiplicitya | 5.4 (5.6) | 5.4 (5.5) |
| Model refinement | ||
| Rworkc | 0.184 | 0.178 |
| Rfreed | 0.228 | 0.226 |
| No. of atoms | 17,702 | 17,447 |
| Avg B-factors (Å2) | ||
| All | 66.0 | 73.0 |
| DNA | 63.3 | 71.9 |
| dNTP | ||
| Chain A | 46.4 (dGTP) | 112.4 (dCTP) |
| Chain C | 53.0 (dGTP) | 97.7 (dCTP) |
| Mg2+ | ||
| Chain A | 47.7 | 42.1 (occupancy = 0.39) |
| Chain C | 48.6 | 144.9 (occupancy = 0.84) |
| RMS deviation from ideal | ||
| Bond lengths (Å) | 0.006 | 0.007 |
| Bond angles (°) | 0.818 | 0.932 |
| Ramachandran plot | ||
| Favored (%) | 96.59 | 96.64 |
| Outliers (%) | 0.16 | 0.16 |
a
The values shown in parentheses are for the outermost resolution shell.
b
Rmeas = ΣhΣi |Ih,i − <Ih>|/ΣhΣi Ih,i, where <Ih> is the mean intensity for a set of equivalent reflections.
c
Rwork = Σ|Fobs – Fcalc|/Σ Fobs for 95% of the reflection data used in the refinement. Fobs and Fcalc are the observed and calculated structure factor amplitudes, respectively.
d
Rfree is the equivalent of Rwork except that it was calculated for a randomly chosen 5% of reflections, which were excluded from refinement.