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Self-assembly of a 3D DNA crystal lattice (4x6 scramble junction version) containing the J26 immobile Holliday junction with R3 symmetry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.5 mL of 0.05 M HEPES pH 7.5 with 15 mM MgCl2, 1.0 mM spermidine, and 10% dioxane was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock
Crystal Properties Matthews coefficient Solvent content 4.83 74.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.088 α = 90 b = 112.088 β = 90 c = 51.133 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 PIXEL DECTRIS EIGER X 16M 2019-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1 NSLS-II 17-ID-1
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 3 50 94.9 0.158 0.166 0.053 0.931 4.3 8.4 4461 62.59
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 3 3.05 64.2 1.184 1.283 0.475 0.525 5.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6XNA 3.015 45.24 1.96 4406 449 93.19 0.2294 0.2259 0.2613 0.2449 71.4773
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 33.677 f_angle_d 0.68 f_chiral_restr 0.031 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 855 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing