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Crystal structure of the Spinach RNA aptamer in complex with DFHBI, magnesium ions
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 3350, 0.5M NaCl, 0.1M succinate-K pH 7.0, 10% sucrose
Crystal Properties Matthews coefficient Solvent content 3.13 60.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.877 α = 90 b = 49.399 β = 90 c = 188.41 γ = 90
Symmetry Space Group P 21 21 21
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 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
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 2.88 50 99.6 23.9 5.1 8415
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 THROUGHOUT 2.884 50 8892 477 99.34 0.2154 0.2129 0.2134 0.2566 0.2543 RANDOM 108.601
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] 1.51 -2.31 0.8
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 6.094 r_angle_other_deg 1.909 r_angle_refined_deg 1.732 r_chiral_restr 0.096 r_gen_planes_refined 0.01 r_bond_refined_d 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1899 Solvent Atoms 5 Heterogen Atoms 68
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction