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Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN 8224 complexed with CGCGAATTCGCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 436D BD0007
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 285 cacodylate, spermine, magnesium chloride, MPD, pH 7.0, VAPOR DIFFUSION, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.188 α = 90 b = 39.868 β = 90 c = 65.961 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH mirror 2004-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.6 50 98.2 0.0433 0.054 22.5 4.5 9114 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 94.3 0.389 2.5 3.6 841
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 refinement THROUGHOUT BD0007 1.6 34.1 9114 8331 747 98.27 0.225 0.225 0.22217 0.2335 0.25832 0.2775 RANDOM 26.529
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] 2.95 -1.41 -1.54
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.002 r_scbond_it 5.923 r_angle_refined_deg 1.693 r_angle_other_deg 1.353 r_nbtor_refined 0.256 r_nbd_other 0.232 r_nbd_refined 0.181 r_symmetry_vdw_other 0.17 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.154
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.002 r_scbond_it 5.923 r_angle_refined_deg 1.693 r_angle_other_deg 1.353 r_nbtor_refined 0.256 r_nbd_other 0.232 r_nbd_refined 0.181 r_symmetry_vdw_other 0.17 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.093 r_nbtor_other 0.093 r_symmetry_vdw_refined 0.07 r_metal_ion_refined 0.046 r_bond_refined_d 0.017 r_gen_planes_refined 0.017 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it 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 522 Solvent Atoms 76 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling