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Four-stranded DNA Holliday Junction (CCC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4Y NDB ENTRY UD0028
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K 2 VAPOR DIFFUSION, SITTING DROP 7 298 Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.96 α = 90 b = 24.71 β = 110.69 c = 36.76 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 103 CCD MARRESEARCH 2004-02-26 M SINGLE WAVELENGTH 2 1 x-ray 103 CCD MARRESEARCH 2004-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.827 APS 14-ID-B 2 SYNCHROTRON APS BEAMLINE 14-ID-B 0.827 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.88 16 88.9 0.103 0.103 8 3883 4.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.88 2.02 65.9 0.335 0.335 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NDB ENTRY UD0028 1.95 16 3477 349 84.3 0.231 0.231 0.2314 0.273 0.2733 RANDOM 11.76
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] -1.016 0.593 -0.946 1.962
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20 c_improper_angle_d 1.79 c_scangle_it 1.568 c_angle_deg 1.3 c_scbond_it 1.1 c_mcangle_it 0.758 c_mcbond_it 0.562 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20 c_improper_angle_d 1.79 c_scangle_it 1.568 c_angle_deg 1.3 c_scbond_it 1.1 c_mcangle_it 0.758 c_mcbond_it 0.562 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 64 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement HKL-2000 data reduction EPMR phasing