Table 1.
Statistics for data collection and refinement
| Data set | SpLCD with NAD+ | SpLCD with NAD+ and L-Pip | SpLCD with NAD+ and L-Pro | SpLCD with NAD+ and DABA |
|---|---|---|---|---|
| A. Data collection | ||||
| X-ray source | PLS7A | PLS7A | SPring-8 BL26B1 | SPring-8 BL26B1 |
| X-ray wavelength (Å) | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| Space group | C2 | C2 | C2 | C2 |
| Unit cell length (a, b, c, Å) | 270.5, 64.4, 106.4 | 271.4, 64.5, 106.3 | 271.5, 64.8, 106.9 | 271.1, 64.8, 106.9 |
| Unit cell angle (Å, β, γ, °) | 90, 104.1, 90 | 90, 104.2, 90 | 90, 104.2, 90 | 90, 104.1, 90 |
| Resolution range (Å) | 50.0–1.92 (1.95–1.92)a | 50–1.92 (1.95–1.92)a | 50–1.79 (1.82–1.79)a | 50–2.14 (2.18–2.14)a |
| Total / unique reflections | 955,775 / 136,288 | 905,894 / 134,717 | 1,267,763/ 169,178 | 689,619 / 97,978 |
| Completeness (%) | 99.6 (98.8)a | 99.3 (98.6)a | 99.9 (98.7)a | 100.0 (100.0)a |
| Average I/σ (I) | 28.6 (4.1)a | 39.6 (12.0)a | 42.2 (4.7)a | 33.3 (4.5)a |
| Rmergeb (%) | 8.2 (50.1)a | 8.9 (42.6)a | 8.0 (50.9)a | 11.3 (75.1)a |
| B. Model refinement | ||||
| Resolution range (Å) | 50.0–1.92 | 50.0–1.92 | 50.0–1.79 | 50.0–2.14 |
| Rwork / Rfreec (%) | 16.8 / 20.0 | 16.7 / 20.3 | 16.4 / 19.3 | 15.9 / 19.7 |
| Monomers per asymmetric unit | 4 | 4 | 4 | 4 |
| Number of non-hydrogen atoms / average B-factor (Å2) | ||||
| Protein | 10,292 / 18.1 | 10,292 / 20.2 | 10,292 / 21.6 | 10,292 / 34.3 |
| Water oxygen | 1,229 / 28.4 | 1,234 / 31.7 | 1,385 / 33.0 | 884 / 41.0 |
| Na+ | 4 / 18.6 | 4 / 22.5 | 4 / 15.6 | 4 / 31.6 |
| NAD+ | 4 / 13.4 | 4 / 14.4 | 4 / 16.3 | 4 / 28.6 |
| L-Pip | - | 4 / 17.9 | - | - |
| L-Pro | - | - | 4 / 25.5 | - |
| DABA | - | - | - | 4 / 42.0 |
| R.m.s. deviations from ideal geometry | ||||
| Bond lengths (Å) / bond angles (°) | 0.008 / 1.39 | 0.008 / 1.41 | 0.008 / 1.48 | 0.008 / 1.39 |
| Protein-geometry analysis | ||||
| Ramachandran favored (%) | 96.8 | 97.5 | 96.8 | 96.8 |
| Ramachandran allowed (%) | 2.9 | 2.2 | 2.9 | 3.1 |
| Ramachandran outliers (%) | 0.3 | 0.3 | 0.3 | 0.1 |
a
Values in parentheses refer to the highest resolution shell.
b
Rmerge = ∑h ∑i | I(h)i – < I(h) > | / ∑h ∑i I(h)i, where I(h) is the intensity of reflection h, ∑h is the sum over all reflections, and ∑i is the sum over i measurements of reflection h.
c
R = ∑hkl | ··· |Fobs| – |Fcalc| | / ∑hkl |Fobs|, where Rfree was calculated for a randomly chosen 5% of reflections, which were not used for structure refinement and Rwork was calculated for the remaining.