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Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN 8315 complexed with CGCGAATTCGCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 436D ndb entry 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 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.873 α = 90 b = 39.907 β = 90 c = 65.707 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 2004-08-18 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 1.8 50 97.2 0.065 0.092 15.3 5.3 6315 35.3
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) 1.8 1.86 98.9 0.511 2.6 2.6 617
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 ndb entry BD0007 1.8 34 9114 5807 473 97.21 0.2405 0.2405 0.23449 0.2316 0.31395 0.3186 RANDOM 39.035
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] 3.62 -1.35 -2.27
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.685 r_scbond_it 8.888 r_angle_refined_deg 1.627 r_angle_other_deg 1.221 r_nbtor_refined 0.245 r_nbd_other 0.224 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_other 0.147 r_metal_ion_refined 0.142
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.685 r_scbond_it 8.888 r_angle_refined_deg 1.627 r_angle_other_deg 1.221 r_nbtor_refined 0.245 r_nbd_other 0.224 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_other 0.147 r_metal_ion_refined 0.142 r_symmetry_hbond_refined 0.12 r_nbtor_other 0.094 r_chiral_restr 0.077 r_symmetry_vdw_refined 0.068 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.005 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 486 Solvent Atoms 33 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling