5YSY
Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2R,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE AR-NE3A |
Synchrotron site | Photon Factory |
Beamline | AR-NE3A |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2011-06-20 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 44.682, 51.538, 132.651 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 2.000 |
R-factor | 0.19196 |
Rwork | 0.189 |
R-free | 0.24223 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1db1 |
RMSD bond length | 0.018 |
RMSD bond angle | 1.729 |
Data reduction software | HKL-2000 |
Data scaling software | SCALA (3.3.20) |
Phasing software | MOLREP (11.0.05) |
Refinement software | REFMAC (5.2.0019) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | |
High resolution limit [Å] | 2.000 | |
Rmerge | 0.096 | 0.431 |
Number of reflections | 21471 | |
<I/σ(I)> | 35.3 | |
Completeness [%] | 99.9 | |
Redundancy | 7.7 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 50mM Mes, 1.4M ammonium sulphate |