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Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J22 immobile Holliday junction with R3 symmetry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.5 mL of 0.05 M Cacodylate pH 6.5 with 36 mM MgCl2, 2.25 mM spermine, and 5% PEG 400 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock
Crystal Properties Matthews coefficient Solvent content 4.74 74.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.022 α = 90 b = 113.022 β = 90 c = 49.338 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 PILATUS3 6M 2018-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.15 50 89 0.076 0.08 0.025 5.5 9.3 3586 93.99
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 3.15 3.2 52 0.29 0.311 0.11 0.974 6.3
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 5VY6 3.163 44.057 2.01 3575 184 88.8 0.2013 0.1999 0.2003 0.2267 0.2221 134.1941
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 32.598 f_angle_d 0.806 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.005
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 PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing