4TS0

Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% PEG 3350, 0.25M NaCl, 0.1M succinate-K pH 7.0, 15% sucrose
Crystal Properties
Matthew coefficientSolvent content
3.0960.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.76α = 90
b = 49.5β = 90
c = 186.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.5498ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.593.1991911.99193

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.850964645399.930.20760.20610.2387RANDOM84.566
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]
1.80.07-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it5.551
r_angle_refined_deg1.958
r_angle_other_deg1.547
r_chiral_restr0.099
r_gen_planes_refined0.011
r_bond_refined_d0.008
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1909
Solvent Atoms15
Heterogen Atoms144

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction