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Crystal Structure of Proflavine in Complex with a DNA hexamer duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z3F PDB Entry 1Z3F (DNA only)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 HEPES, Cobalt Hexamine, MPD, PEG1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 1.88 34.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.563 α = 90 b = 24.563 β = 90 c = 78.276 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2007-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0000 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 21.27 93.4 0.052 44.8 9.1 10189 10189
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) 1.1 1.14 52.4 0.334 1.75 3.5 569
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 (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 Entry 1Z3F (DNA only) 1.12 20.53 8808 1096 96.57 0.18811 0.18433 0.1925 0.21929 0.227 RANDOM 15.446
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]
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 5.27 r_scangle_it 2.782 r_scbond_it 2.325 r_rigid_bond_restr 1.926 r_angle_refined_deg 1.732 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.165 r_nbd_refined 0.132 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.118
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 5.27 r_scangle_it 2.782 r_scbond_it 2.325 r_rigid_bond_restr 1.926 r_angle_refined_deg 1.732 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.165 r_nbd_refined 0.132 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.091 r_gen_planes_refined 0.022 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 37 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement CNS refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing