High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| 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 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.38 | 48.38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 108.912 | α = 90 |
| b = 108.912 | β = 90 |
| c = 34.812 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2013-11-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.978 | EMBL/DESY, HAMBURG | X13 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||||
| 1 | 2.05 | 100 | 99.2 | 24915 | -3 | 36.4 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.05 | 77.01 | 12058 | 1348 | 97.9 | 0.20504 | 0.20003 | 0.201 | 0.24971 | 0.2498 | RANDOM | 32.728 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.21 | 0.21 | -0.41 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.662 |
| r_dihedral_angle_4_deg | 25.514 |
| r_dihedral_angle_3_deg | 14.378 |
| r_dihedral_angle_1_deg | 5.36 |
| r_long_range_B_refined | 5.024 |
| r_mcangle_it | 3.633 |
| r_mcbond_it | 2.098 |
| r_angle_refined_deg | 1.609 |
| r_scbond_it | 1.536 |
| r_chiral_restr | 0.074 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 544 |
| Nucleic Acid Atoms | 853 |
| Solvent Atoms | 111 |
| Heterogen Atoms | 7 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MxCuBE | data collection |
| PHENIX | model building |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
