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Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Grown by vapor diffusion while treated with a controlled temperature gradient from 333K degs to 293K. They were grown in Ammonium Sulfate, TRIS, Acetic Acid and EDTA.
Crystal Properties Matthews coefficient Solvent content 3.75 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.712 α = 90 b = 106.712 β = 90 c = 94.081 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 CCD ADSC QUANTUM 315 2013-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.1 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.05 50 68 0.107 10.8 7.8 5152 90.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.1 19.2 0.431 6.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3GBI 3.06 32.96 1.96 5137 507 68 0.225 0.223 0.2383 0.241 0.2522 Random 120.6
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 39.734 f_angle_d 1.451 f_chiral_restr 0.082 f_bond_d 0.016 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 859 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction