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Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal B type DNA duplexes generated in Cadnano
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.5 ug/uL motif
0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium, 0.16 M lithium sulfate monohydrate, 3 % MPD at pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.38 63.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.97 α = 90 b = 37.97 β = 90 c = 69.554 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2022-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.61 32.883 80 1 17.3 7.5 1876 57.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.948 0.59
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 ideal B type DNA duplexes generated in Cadnano 2.61 29.73 1.97 1871 86 54.8 0.2197 0.2156 0.216 0.2926 0.2854 42.58
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 40.8527 f_angle_d 1.7152 f_chiral_restr 0.087 f_bond_d 0.0133 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 568 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction STARANISO data scaling PHASER phasing