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A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K8P PDB Entry 1K8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285.15 1.6 mM DNA, 1.6 mM BRACO19, 200 mM ammonium sulphate, 20 mM sodium chloride, 20 mM potassium chloride, 20 mM lithium sulphate and 36 mM potassium cacodylate buffer at pH 6.5 equilibrated against 1.6 M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 285.15K
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.338 α = 90 b = 70.338 β = 90 c = 34.293 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV mirrors 2008-01-15 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) 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 2.5 35.17 99.7 0.065 9.8 2.9 3003 2994 3 58.2
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 2.5 2.59 100 0.31 2.4 2.8 291
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 MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1K8P 2.5 35.17 2992 2852 140 100 0.18446 0.18446 0.18298 0.1792 0.21341 0.2122 RANDOM 23.482
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] 2.08 2.08 -4.15
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.864 r_scbond_it 2.845 r_angle_refined_deg 2.813 r_nbtor_refined 0.342 r_nbd_refined 0.306 r_xyhbond_nbd_refined 0.207 r_symmetry_hbond_refined 0.196 r_symmetry_vdw_refined 0.193 r_metal_ion_refined 0.162 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.864 r_scbond_it 2.845 r_angle_refined_deg 2.813 r_nbtor_refined 0.342 r_nbd_refined 0.306 r_xyhbond_nbd_refined 0.207 r_symmetry_hbond_refined 0.196 r_symmetry_vdw_refined 0.193 r_metal_ion_refined 0.162 r_chiral_restr 0.115 r_bond_refined_d 0.024 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 502 Solvent Atoms 54 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing