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 |