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Crystal structure of the complex of DNA hexamer d(CGATCG) with Coptisine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FT6 PDB ENTRY 3FT6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 296 10% MPD, 40 mM Na Cacodylate, 12 mM spermine tetra-HCl, 80 mM sodium chloride and 20 mM barium chloride, pH 6.0, vapor diffusion, sitting drop, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.18 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.581 α = 90 b = 26.581 β = 90 c = 77.094 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD OXFORD ONYX CCD 2011-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.542
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 2.7 14.78 97 0.092 18.99 558 -3
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 2.99 3.16 87.9 0.776 3.69
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3FT6 2.71 14.78 558 98.59 0.2671 0.2671 0.2673 93.273
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] 2.11 1.06 2.11 -6.85
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 10.411 r_angle_refined_deg 2.922 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 10.411 r_angle_refined_deg 2.922 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 120 Solvent Atoms 3 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling