4R8I
High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | EMBL/DESY, HAMBURG BEAMLINE X13 |
Synchrotron site | EMBL/DESY, Hamburg |
Beamline | X13 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2013-11-14 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.978 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 108.912, 108.912, 34.812 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 77.010 - 2.050 |
R-factor | 0.20504 |
Rwork | 0.200 |
R-free | 0.24971 |
Structure solution method | SAD |
RMSD bond length | 0.011 |
RMSD bond angle | 1.609 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX |
Refinement software | REFMAC (5.8.0073) |
Data quality characteristics
Overall | |
Low resolution limit [Å] | 100.000 |
High resolution limit [Å] | 2.050 |
Number of reflections | 24915 |
Completeness [%] | 99.2 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | After thorough optimization of crystallization conditions needle shaped crystals (approx. 300x50x50um) could be obtained by mixing 1uL of the NOX-E36-CCL2 complex (in 20 mM HEPES pH 7.4, 100 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2) with 1uL of a solution containing 40 mM Na cacodylate pH 5.5, 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2 and subsequent vapor-diffusion equilibration against 1 mL of reservoir (35% (v/v) MPD, 5 mM KCl, 1 mM MgCl2 and 1 mM CaCl2). Crystals used for data collection grew within three weeks at 277K. VAPOR DIFFUSION, HANGING DROP, temperature 277K |