Table 1. Data collection and refinement statistics.
| Dataset | NagR + GlcN-6-P | NagR + GlcNAc-6-P | NagR + 19mer dsDNA | NagR–DBD + 15mer dsDNA |
|---|---|---|---|---|
| Data collectiona | ||||
| Beamline | BESSY-MX, BL 14.1 | |||
| Wavelength (Å) | 0.91841 | |||
| Resolution (Å) | 35.00–2.05 | 35.00–2.00 | 35.00–2.90 | 35.00–1.91 |
| (2.12–2.05) | (2.07–2.00) | (3.01–2.90) | (1.98–1.91) | |
| Space group | R32 :H | R32 :H | P43212 | P31 |
| Cell parameters (Å/°) | 98.5/98.5/355.1 | 99.1/99.1/354.0 | 80.0/80.0/240.0 | 48.6/48.6/153.9 |
| 90/90/120 | 90/90/120 | 90/90/90 | 90/90/120 | |
| Total reflections | 182317 (17692) | 512951 (50379) | 127822 (12058) | 120087 (11497) |
| Unique reflections | 42017 (4067) | 45784 (4525) | 18046 (1754) | 31230 (3069) |
| Redundancy | 4.3 (4.4) | 11.2 (11.1) | 7.1 (6.9) | 3.8 (3.7) |
| Completeness (%) | 99.8 (98.6) | 99.9 (99.8) | 99.9 (99.8) | 99.8 (98.7) |
| I/σ(I) | 19.4 (2.4) | 20.2 (2.4) | 16.8 (1.2) | 10.6 (1.9) |
| Wilson B-value (Å2) | 34.8 | 36.0 | 90.1 | 25.8 |
| Rmergeb (%) | 5.8 (65.6) | 8.9 (126.4) | 9.9 (197.9) | 8.5 (86.5) |
| Rmeasc (%) | 6.6 | 9.4 | 10.7 | 9.9 |
| CC1/2d (%) | 99.9 (74.6) | 99.9 (90.5) | 99.9 (29.4) | 99.7 (67.8) |
| Structure refinement | ||||
| Resolution (Å) | 32.65–2.05 | 32.73–2.00 | 34.28–2.90 | 32.52–1.91 |
| Rwork/Rfree (%)e | 19.97/24.78 | 20.65/25.30 | 22.89/27.78 | 17.84/22.93 |
| No. of non-hydrogen atoms | 4284 | 4246 | 4350 | 3350 |
| No. of protein residues | 485 | 486 | 443 | 329 |
| No. of solvent molecules | 285 | 253 | 2 | 287 |
| Additional molecules | 2 × GlcN-6-P | 2 × GlcNAc-6-P | 1 × 19mer dsDNA | 1 × 15mer dsDNA |
| 25 × ethylene glycol | 13 × ethylene glycol | 7 × ethylene glycol | 2 × chloride ion | |
| 2 × glycerol | ||||
| Average B-factors (Å2) | 38.5 (all atoms) | 41.3 (all atoms) | 85.0 (all atoms) | 29.9 (all atoms) |
| 38.0 (protein) | 41.0 (protein) | 85.3 (protein + DNA) | 29.4 (protein + DNA) | |
| 44.0 (water) | 45.1 (water) | 58.7 (water) | 34.3 (water) | |
| 42.1 (ligands) | 44.4 (ligands) | 81.1 (ligands) | 22.9 (ligands) | |
| Ramachandran favored (%) | 98.5 | 98.6 | 96.0 | 98.3 |
| Ramachandran outliers (%) | 0.0 | 0.0 | 1.2 | 0.0 |
| R.m.s. deviations | ||||
| Bonds lengths (Å) | 0.008 | 0.008 | 0.011 | 0.007 |
| Bond angles (°) | 1.137 | 1.096 | 1.430 | 1.087 |
aValues for the highest resolution shell are listed in parentheses.
bRmerge = Σ|I − <I>|/ΣI, where I is the integrated intensity of a given reflection.
cRmeas is the multiplicity weighted merging R-factor.
dCorrelation coefficient between two random halves of the dataset as described by Karplus and Diederichs (24), and calculated using XDS (23).
eRwork = Σ∥Fobs| − |Fcalc∥/Σ|Fobs|. Rfree was calculated using 5% of data excluded from refinement.