Table I. Summary of data collection and refinement statistics for VDR–DNA complexes.
| Diffraction data/Complex | SPP | DR3 | OC | |||
|---|---|---|---|---|---|---|
| Source | APS-14BMC | APS-19BM | APS-19BM | APS-19BM | APS-19BM | APS-19BM |
| Space group | P43212 | P43212 | P43212 | |||
| a, c (Å) | 62.14, 241.75 | 61.81, 242.34 | 61.15, 241.80 | |||
| Wavelength (Å) | 1.0000 | 1.2828 | 1.0332 | 1.2828 | 1.0332 | 1.2828 |
| Resolutiona (Å) | 50–2.70 | 50–3.1 | 50–2.80 | 50–3.0 | 50–2.70 | 50–3.0 |
| Last shell (Å) | 2.80–2.70 | 3.21–3.10 | 2.90–2.80 | 3.11–3.00 | 2.80–2.70 | 3.11–3.00 |
| Unique reflections | 13 744 | 16 105 | 12 384 | 17 291 | 13 127 | 17 551 |
| Completeness (%) | 98.2 (99.9) | 99.8 (98.9) | 99.5 (99.0) | 96.9 (86.0) | 96.7 (77.6) | 99.7 (99.0) |
| Average I/σI | 22.9 (2.3) | 18.9 (3.0) | 27.2 (2.3) | 27.1 (2.1) | 34.4 (2.9) | 25.8 (3.9) |
| Redundancy | 5.9 | 8.3 | 14.1 | 12.6 | 12.5 | 5.3 |
| Rmergeb (%) | 8.1 (76) | 11.1 (27) | 10.0 (39) | 9.9 (48) | 7.1 (32) | 6.3 (36) |
| Phasing powerc | 1.31 | 1.74 | 1.50 | |||
| FOM (after DM)d |
|
0.18 (0.97) |
|
0.25 (0.85) |
0.23 (0.92) | |
| Crystallographic refinement | ||||||
| Resolution range (Å) | 50–2.70 | 50–2.80 | 50–2.70 | |||
| Reflections (F >2σF) | 12 490 (10 433) | 11 200 (9350) | 11 999 (10 321) | |||
| Non-solvent atoms | 2100 | 2204 | 2237 | |||
| Solvent atoms | 35 | 31 | 34 | |||
| Protein model (upstream/downstream) | 22–110/22–106 | 22–114/22–120 | 21–114/21–121 | |||
| Side chains truncated to alanine | 4/5 | 6/14 | 6/12 | |||
| R.m.s. deviation from ideality | ||||||
| Bond lengths (Å) | 0.0146 | 0.0154 | 0.0157 | |||
| Bond angles (°) | 1.66 | 1.69 | 1.78 | |||
| R-value (F >2σF)e (%) | 22.6 (20.9) | 21.4 (19.6) | 22.3 (20.6) | |||
| Rfree (F >2σF) | 28.9 (27.0) | 27.2 (25.4) | 27.5 (25.8) | |||
aThe resolution limit was defined as I/σI ≥2.0.
bRmerge = ∑hkl∑i|Ii(hlk) – <I(hkl)>|/∑hkl∑II(hkl).
cPhasing power = <[|FH|/E]>, where E is the residual lack of closure.
dFigure of merit = <|∑P(α)eiα/∑P(α)|>, where α is the phase and P(α) is the phase probability distribution.
eR = ∑|Fo – Fc|/∑Fo: 10% of reflections were used to calculate Rfree.