Table 1.
Crystallographic statistics of the YugJ structures.
| YugJNi | YugJNADP-Ni | YugJNADP-NO3 | |
|---|---|---|---|
| Data collection | |||
| Space group | P212121 | P1 | P21 |
| Cell parameters | |||
| a (Å) | 62.66 | 66.04 | 56.51 |
| b (Å) | 114.52 | 69.64 | 67.69 |
| c (Å) | 118.74 | 87.61 | 102.37 |
| α (°) | 90 | 92.29 | 90 |
| β (°) | 90 | 91.03 | 100.15 |
| γ (°) | 90 | 90.37 | 90 |
| Wavelength (Å) | 1.0000 | 0.9793 | 1.0000 |
| Resolution (Å) | 30.00–2.15 | 30.00–1.93 | 30.00–1.65 |
| Highest resolution (Å) | 2.19–2.15 | 1.96–1.93 | 1.68–1.65 |
| No. uniquere flections | 47,100 (2297) a | 112,718 (5537) a | 91,189 (4474) a |
| Rmerge (%) b | 6.8 (50.0) a | 5.5 (35.1) a | 7.7 (44.1) a |
| Rmeas (%) c | 7.6 (55.8) a | 7.8 (49.7) a | 9.0 (51.7) a |
| CC1/2 d | 0.997 (0.860) a | 0.997 (0.740) a | 0.994 (0.879) a |
| I/sigma(I) | 32.6 (5.0) a | 19.1 (2.8) a | 27.4 (4.2) a |
| Completeness (%) | 99.9 (100.0) a | 96.7 (95.3) a | 99.6 (99.0) a |
| Redundancy | 4.9 (5.0) a | 2.0 (1.9) a | 3.7 (3.7) a |
| Wilson B-factor (Å2) | 33.4 | 22.1 | 16.4 |
| Refinement | |||
| Resolution (Å) | 30.00–2.15 | 30.00–1.93 | 30.00–1.65 |
| No. of reflections (work) | 44,658 | 106,897 | 86,549 |
| No. of reflections (test) | 2376 | 5775 | 4572 |
| Rwork (%) e | 20.3 | 17.0 | 17.4 |
| Rfree (%) f | 24.1 | 20.8 | 19.7 |
| Estimated coordinate error (Å) | 0.25 | 0.19 | 0.16 |
| No. atoms | |||
| Protein | 5717 | 11,878 | 5897 |
| Metals | 2 | 4 | - |
| NADP | - | 160 | 96 |
| Nitrate | - | - | 16 |
| Water | 116 | 792 | 605 |
| Average B-value (Å2) | |||
| Protein | 49.0 | 29.2 | 21.6 |
| Metals | 51.1 | 26.8 | - |
| NADP | - | 22.8 | 13.8 |
| Nitrate | - | - | 23.3 |
| Water | 37.0 | 32.5 | 29.7 |
| RMSD bonds (Å) | 0.008 | 0.007 | 0.006 |
| RMSD angles (°) | 0.864 | 0.851 | 0.899 |
| Ramachandran g (favored) | 97.4% | 97.5% | 96.8% |
| Ramachandran g (outliers) | 0.0% | 0.1% | 0.0% |
| PDB ID | 7W9X | 7W9Y | 7W9Z |
a Numbers in parentheses were calculated from data for the highest resolution shell. b Rmerge = ΣhklΣi|Ii(hkl)—<I(hkl)> |/ΣhklΣi Ii(hkl); c Rmeas = Σhkl{N(hkl)/[N(hkl)—1]}1/2 Σi | Ii(hkl)—<I(hkl)>|/ΣhklΣi Ii(hkl); d Correlation coefficient between intensities from random half-data sets. e Rwork = Σ||Fobs|-|Fcalc||/Σ|Fobs| where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively. f Rfree = as described for Rwork, except that 5% of the total reflections were selected at random and omitted from refinement. g Calculated using MolProbity (http://molprobity.biochem.duke.edu, accessed on 11 December 2021).