Table 2. Data collection and refinement statistics.
| mPDXP-7,8-DHF with phosphate(8QFW) | hPDXP-7,8-DHF with phosphate(9EM1) | hPDXP-7,8-DHF without phosphate(8S8A) | |
|---|---|---|---|
| Data collection | |||
| Space group | I23 | P43212 | P43212 |
| a, b, c (Å) | 167.01, 167.01, 167.01 | 53.96, 53.96, 211.75 | 54.04, 54.04, 212.49 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å) | 47.21–2.00 (2.07–2.00) | 48.08–1.50 (1.53–1.50) | 48.17–1.50 (1.53–1.50) |
| Rsym* | 0.190 (4.101) | 0.126 (4.893) | 0.081 (3.670) |
| Rpim† | 0.030 (0.652) | 0.018 (0.689) | 0.017 (0.731) |
| CC1/2 | 1.00 (0.459) | 0.991 (0.526) | 0.999 (0.579) |
| <I/σI>‡ | 20.7 (1.1) | 24.6 (1.4) | 17.5 (1.1) |
| Completeness | 0.998 (0.973) | 1.00 (1.00) | 1.00 (1.00) |
| Redundancy | 41.0 (38.5) | 50.7 (51.0) | 25.6 (26.0) |
| Refinement | |||
| Resolution (Å) | 20.00–2.00 (2.07–2.00) | 38.16–1.50 (1.55–1.50) | 48.165–1.50 (1.55–1.50) |
| R-work§ | 0.1838 (0.300) | 0.1702 (0.2740) | 0.1817 (0.2938) |
| R-free¶ | 0.21 (0.322) | 0.1939 (0.3217) | 0.2050 (0.2955) |
| RMS deviations in | |||
| Bond lengths (Å) | 0.002 | 0.012 | 0.005 |
| Bond angles (°) | 0.50 | 1.08 | 0.80 |
| Chiral centers (Å3) | 0.038 | 0.065 | 0.046 |
| Planar groups (Å) | 0.005 | 0.014 | 0.010 |
| Estimated coordinate error (Å) | 0.26 | 0.16 | 0.19 |
| Ramachandran statistics (%) | 98.95/1.05/0 | 98.63/1.37/0 | 98.63/1.37/0 |
Numbers in parentheses refer to the highest resolution data shell.
Ramachandran statistics reflect the percentage of residues in favored/allowed/outlier regions. Source data (raw diffraction images) have been deposited in the Xtal Raw Data Archive and can be accessed under the XRDA entries 8QFW (https://xrda.pdbj.org/entry/8qfw), 9EM1 (https://xrda.pdbj.org/entry/9em1), and 8S8A (https://xrda.pdbj.org/entry/8s8a).
Rsym = ΣhklΣi | Ii – <I> |/ΣhklΣiIi where Ii is the ith measurement and <I> is the weighted mean of all measurements of I.
Rpim = Σhkl1/(N – 1)½ Σi|Ii(hkl) – I(hkl)|/ΣhklΣiI(hkl), where N is the redundancy of the data and I(hkl) the average intensity.
<I/σI> indicates the average of the intensity divided by its standard deviation.
Rwork = Σhkl ||Fo| – |Fc||/Σhkl|Fo| where Fo and Fc are the observed and calculated structure factor amplitudes.
Rfree same as R for 5% of the data randomly omitted from the refinement. The number of reflections includes the Rfree subset.