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DNA Holliday junction stabilized by fluorine halogen bond. F2J 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 Properties Matthews coefficient Solvent content 2.27 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.213 α = 90 b = 23.917 β = 114.8 c = 77.45 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 2011-01-01 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) R Merge I (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 2.04 55 24.9 0.066 23 5.5 6763 3910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.13 3.3 0.207 3.4 26
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 2.38 32.61 4947 3398 180 74.2 0.225 0.2248 0.291 0.3052 RANDOM 15.9929
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] 2.48 0.88 3.58 -6.06
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.7 c_improper_angle_d 1.02 c_angle_deg 0.6 c_bond_d 0.002 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 1616 Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction CNS phasing