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Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J19 immobile Holliday junction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.5 mL of 0.05 M Cacodylate pH 7.0 with 20 mM MgCl2, 1.0 mM spermine, 1.0 mM CoH18N6, and 15% Ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock
Crystal Properties Matthews coefficient Solvent content 3.22 61.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.513 α = 90 b = 68.513 β = 90 c = 60.773 γ = 120
Symmetry Space Group P 32 2 1
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 DECTRIS PILATUS3 6M 2017-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
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 2.75 50 99.6 0.112 0.118 0.036 0.957 11.5 11.3 4478 96.98
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 2.75 2.8 98.6 1.675 1.758 0.526 0.652 9.3
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 THROUGHOUT 5KEK 2.756 34.257 1.38 4413 234 98.39 0.212 0.2109 0.2181 0.2328 0.2415 103.6796
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 35.14 f_angle_d 0.992 f_chiral_restr 0.053 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 855 Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing