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Crystal structures of Cy3 cyanine fluorophores stacked onto the end of double-stranded RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 50 mM sodium cacodylate at pH 6.5,
100 mM Mg(CH3COO)2,
50 mM KF,
15% PEG 8000 drop
Crystal Properties Matthews coefficient Solvent content 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.757 α = 90 b = 122.432 β = 90 c = 51.013 γ = 90
Symmetry Space Group P 21 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 93 PIXEL DECTRIS PILATUS3 S 6M 2013-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979601 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 46.88 100 0.09978 0.1141 12.48 4.4 23654 48.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.486 100 0.162 0.1834 6.26 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1MJI 2.4 46.88 1.35 23593 1195 99.57 0.261 0.2598 0.2642 0.283 0.2845 37.1008
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.6 f_angle_d 1.531 f_chiral_restr 0.096 f_bond_d 0.013 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms 1325 Solvent Atoms 72 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHENIX phasing