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DNA Holliday junction stabilized by chlorine halogen bond. Cl1J construct of 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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.578 α = 90 b = 24.355 β = 110.85 c = 37.243 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 CCD NOIR-1 2009-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.9 ALS 4.2.2
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 1.7 50 79.2 6244 4947 1.4 2 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2 30.64 6244 3667 212 94.8 0.271 0.2743 0.322 0.3233 RANDOM 14.3574
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] 1.8 -0.94 3.64 -5.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.5 c_scangle_it 2.42 c_scbond_it 1.77 c_improper_angle_d 0.88 c_angle_deg 0.4 c_bond_d 0.001 c_mcbond_it c_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 808 Solvent Atoms 159 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing