1KB4
Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-BM |
| Synchrotron site | APS |
| Beamline | 19-BM |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2001-09-15 |
| Detector | APS-1 |
| Wavelength(s) | 1.0332 |
| Spacegroup name | P 43 21 2 |
| Unit cell lengths | 61.500, 61.500, 241.970 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 50.000 - 2.800 |
| R-factor | 0.214 * |
| Rwork | 0.214 |
| R-free | 0.27200 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | TR Half-Complex from PDB Entry 2NLL |
| RMSD bond length | 0.015 |
| RMSD bond angle | 1.690 * |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | CNS |
| Refinement software | CNS |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.900 |
| High resolution limit [Å] | 2.800 | 2.800 |
| Rmerge | 0.100 | 0.390 |
| Number of reflections | 12384 | |
| <I/σ(I)> | 27.2 | 2.3 |
| Completeness [%] | 99.5 | 99 |
| Redundancy | 14.1 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.6 * | 18 * | PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | PEG 8000 | ||
| 2 | 1 | 1 | MgCl2 | ||
| 3 | 1 | 1 | MES | ||
| 4 | 1 | 1 | glycerol | ||
| 5 | 1 | 1 | DTT |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | protein | 0.33-0.66 (mM) | |
| 2 | 1 | drop | Tris | 5 (mM) | pH7.6 |
| 3 | 1 | drop | 50 (mM) | ||
| 4 | 1 | drop | dithiothreitol | 2 (mM) | |
| 5 | 1 | reservoir | PEG4000 | 4-6 (%) | |
| 6 | 1 | reservoir | MES | 50 (mM) | pH5.6 |
| 7 | 1 | reservoir | 5 (mM) | ||
| 8 | 1 | reservoir | glycerol | 10 (%) | |
| 9 | 1 | reservoir | dithiothreitol | 10 (mM) |
