Table 1.
Data collection and refinement statistics
| Crystal type | SeMet | Closed | Open | |||
|---|---|---|---|---|---|---|
| Crystallization | ||||||
| Precipitant | PEG 1500 (~30%) | PEG 1500 (~30%) | MPD (~25%) | |||
| Buffer | HEPES (50 mM) pH 6.6 | ADA (100 mM) pH 6.5 | MES (100 mM) pH 5.7 | |||
| [Na+] | ~5 mM | ~100 mM | ~100 mM | |||
| Cell parameters | a=78.52 Å b=96.12 Å c=78.05 Å β=118.49° |
a=78.24 Å b=95.60 Å c=77.90 Å β =118.30° |
a=87.71 Å b=90.57 Å c=85.40 Å β =118.54° |
|||
| Data collection | ||||||
| Wavelength (Å) | 0.9791 | 0.9794 | 0.95000 | 1.0000 | 0.9000 | 0.9000 |
| Data set | λ1 (peak) | λ2 (inflection) | λ3 (remote high) | λ4 (remote low) | ||
| Resolution range (Å)a | 50-1.75 | 50-1.75 | 50-1.75 | 50-1.75 | 1.15 | 1.9 |
| # Reflections | 384455 | 376632 | 374339 | 374960 | 851037 | 155334 |
| # Unique reflections | 51037 | 50987 | 50823 | 50708 | 160538 | 43421 |
| Rmerge (%)b | 6.8 (30.4) | 7.3 (36.6) | 7.0 (47.3) | 7.0 (42.5) | 4.7 (20.5) | 3.9 (20.0) |
| Completeness (%) | 99.7 (99.5) | 99.6 (98.0) | 99.3 (94.7) | 99.3 (95.7) | 90.0 (46.1) | 92.8 (60.2) |
| Anomalous completeness (%) | 98.7 | 98.4 | 97.5 | |||
| <I/σ(I)>c | 33.6 (5.9) | 30.9 (4.1) | 28.7 (2.8) | 28.3 (3.4) | 27.3 (4.5) | 29.8 (5.0) |
| Redundancy | 3.8 | 3.7 | 3.7 | 3.7 | 5.3 | 3.6 |
| Phasing | ||||||
| Ranomalousd | 0.37 | 0.34 | 0.43 | |||
| (wavelengths) | λ1-λ2 | λ1-λ3 | λ2-λ3 | |||
| Rcentrice | 0.72 | 0.66 | 0.76 | |||
| Phasing power | 1.3 | 1.9 | 1.2 | |||
| Refinement | ||||||
| Resolution range | 50-1.75 Å | 50-1.15 Å | 50-1.9 Å | |||
| Rworkf | 0.191 | 0.127 | 0.185 | |||
| # reflections | 47300 | 152457 | 40971 | |||
| Rfreeg | 0.228 | 0.153 | 0.217 | |||
| # reflections | 2501 | 8054 | 2142 | |||
| # protein atoms | 3006 | 3028 | 3081 | |||
| # FAD atoms | 53 | 53 | 53 | |||
| #ligand atoms | 9 | 9 | 9 | |||
| #other atomsh | 0 | 1 | 16 | |||
| # water molecules | 264 | 431 | 266 | |||
| B-factors | ||||||
| Protein (Å2) | 28.1 | 20.2 | 27.6 | |||
| Ligands (Å2) | 18.0 | 14.4 | 26.7 | |||
| Water (Å2) | 38.8 | 34.8 | 35.5 | |||
| All (Å2) | 28.8 | 21.9 | 28.2 | |||
| RMSD | ||||||
| Bonds (Å) | 0.010 | 0.019 | 0.010 | |||
| B-factor bonds (Å2) | 2.9 | 3.6 | 2.2 | |||
| Δ B main-main (Å2) | 2.1 | 2.1 | 1.7 | |||
| Δ B side-side (Å2) | 3.7 | 5.0 | 2.6 | |||
| Δ B main-side (Å2) | 2.9 | 3.5 | 2.0 | |||
| Ramachandran plot | ||||||
| Most favored | 90.7% | 92.3% | 92.2% | |||
| Additional allowed | 9.0% | 7.4% | 7.5% | |||
| Generously allowed | 0.3% | 0.3% | 0.3% | |||
Values in parentheses refer to the highest resolution shell.
Rmerge (I)= Σ|Ii - <I>| /ΣIi, where Ii is the intensity of the ith observation, <I> is the mean intensity of the reflection, and the summation extends over all data.
I/σ(I) is the average signal to noise ratio for merged reflection intensities.
MAD phasing statistics for f“
MAD phasing statistics for f’
R-factor= Σ||Fo|-|Fc||/Σ|Fo|, where |Fo| is observed structure factor amplitudes and |Fc| is calculated structure factor amplitudes and the summation extends over all data.
Rfree is the R-factor obtained for a test set of reflections, consisting of a randomly selected 5% subset of the diffraction data, not used during refinement.
The closed form of nikD contains one sodium ion and the open form contains two molecules of MPD