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DNA Holliday junction stabilized by iodine halogen bond. I1J construct in related reference.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ORG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 298 0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.739 α = 90 b = 25.187 β = 110.88 c = 37.171 γ = 90
Symmetry Space Group C 1 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 133 IMAGE PLATE RIGAKU RAXIS 2004-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 50 73.9 4645 3432 1.4 2 18.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 THROUGHOUT 2ORG 1.9 23.3 1.4 4645 3423 345 73.7 0.235 0.2204 0.261 0.2654 RANDOM 31.4219
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] -6.64 -0.06 7.2 -0.56
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_improper_angle_d 1.4 c_angle_deg 0.9 c_bond_d 0.005 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction