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Structure of Holliday junction formed by d(CCGGTACCGG); Crystal grown with CoCl2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JUC PDB ID 1JUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1mM DNA, 50mM Sodium Cacodylate buffer, 1mM CoCl2, 10mM spermine, 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.002 α = 90 b = 24.76 β = 110.62 c = 37.369 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 100 IMAGE PLATE MARRESEARCH Mirrors 2009-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.5 28.44 92.9 0.096 0.075 4.1 2.84 1893 1864 1 63.2
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) 2.5 2.6 90.1 0.304 0.262 1.4 3.08 172
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-Factor (All) 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 PDB ID 1JUC 2.51 28.44 1864 1760 104 92.78 0.24057 0.24057 0.23971 0.2418 0.25408 0.2517 RANDOM 33.891
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] -1.29 0.01 1.65 -0.35
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.828 r_scangle_it 2.527 r_scbond_it 2.479 r_nbtor_refined 0.348 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.23 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.105 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.828 r_scangle_it 2.527 r_scbond_it 2.479 r_nbtor_refined 0.348 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.23 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling