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Crystal structure of RNA G2C4 repeats in complex with small synthetic molecule ANP77
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 0.08 M NaCl, 0.04 M Na cacodylate trihydrate pH 6.0, 45% v/v MPD, 0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 1.92 35.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.343 α = 90 b = 45.179 β = 90 c = 86.28 γ = 90
Symmetry Space Group C 2 2 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 RIGAKU HyPix-6000HE 2020-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.1 21.85 99.9 0.076 0.081 0.025 0.999 26.9 16.3 23771 8.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 0.56 0.617 0.254 0.894 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.1 21.85 1.34 23685 479 99.71 0.1227 0.1218 0.1219 0.1737 0.174 13.03
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 11.754 f_angle_d 1.384 f_chiral_restr 0.0661 f_plane_restr 0.0142 f_bond_d 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms 105 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PHENIX refinement CrysalisPro data reduction SCALA data scaling PHASER phasing