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Crystal Engineering with One 8-mer DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other 7 bp ideal B type DNA duplex generated in Cadnano
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 4 uL 0.5 ug/uL DNA motif in 0.2* TAE/Mg2+ buffer (annealing from 95-22 degree C in 2 hours) + 5 uL crystallization buffer [2 mM magnesium chloride hexahydrate, 4 mM sodium cacodylate trihydrate, pH 5.5, 4% v/v MPD, 0.2 mM hexammine cobalt (III) chloride]
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.639 α = 90 b = 69.639 β = 90 c = 72.756 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++ 2021-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.54178
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 2.17 46.43 83.9 1 15.8 13.4 2537
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 2.17 2.4 0.466 1.4
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 7 bp ideal B type DNA duplex generated in Cadnano 2.17 31.15 1.36 2527 126 67.98 0.2512 0.2508 0.2511 0.2608 0.2549 31.19
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 34.5833 f_angle_d 0.7931 f_chiral_restr 0.0578 f_bond_d 0.0071 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 483 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction STARANISO data scaling PHASER phasing