3A78
Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ESRF BEAMLINE ID29 |
| Synchrotron site | ESRF |
| Beamline | ID29 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2008-04-20 |
| Detector | ADSC QUANTUM 315r |
| Wavelength(s) | 0.975531 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 44.889, 51.120, 132.196 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 30.000 - 1.900 |
| R-factor | 0.17385 |
| Rwork | 0.172 |
| R-free | 0.20307 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1db1 |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.130 |
| Data reduction software | MOSFLM |
| Data scaling software | SCALA |
| Phasing software | REFMAC (5.2.0019) |
| Refinement software | REFMAC (5.2.0019) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 48.000 | 2.000 |
| High resolution limit [Å] | 1.900 | 1.900 |
| Rmerge | 0.078 | 0.240 |
| Number of reflections | 23145 | |
| <I/σ(I)> | 11.3 | 3.5 |
| Completeness [%] | 94.3 | 92.4 |
| Redundancy | 2.5 | 2.4 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 10mM Tris, 100mM NaCl, 1mM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
