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ATC Four-stranded DNA Holliday Junction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZEZ ndb entry UD0058
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
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.95 α = 90 b = 24.62 β = 112.09 c = 37.46 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 ADSC QUANTUM 4 2004-02-26 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9795 APS 14-BM-D
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 1.84 99 98.6 0.061 0.061 15 4856
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 1.84 1.92 96.9 96.9 0.626 0.626 1.07
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 (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 ndb entry UD0058 1.84 30.08 4063 472 100 0.205 0.248 0.202 0.2014 0.231 0.2324 RANDOM 9.615
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] -0.1 -0.1 0.33 -0.3
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.663 r_scangle_it 1.589 r_scbond_it 1.251 r_nbtor_refined 0.31 r_nbd_refined 0.278 r_xyhbond_nbd_refined 0.271 r_symmetry_vdw_refined 0.237 POTENTIAL METAL-ION REFINED ATOMS (A) 0.223 r_symmetry_hbond_refined 0.207 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.663 r_scangle_it 1.589 r_scbond_it 1.251 r_nbtor_refined 0.31 r_nbd_refined 0.278 r_xyhbond_nbd_refined 0.271 r_symmetry_vdw_refined 0.237 POTENTIAL METAL-ION REFINED ATOMS (A) 0.223 r_symmetry_hbond_refined 0.207 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 150 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement HKL-2000 data reduction EPMR phasing