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The first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a copper complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 Initial conditions were 0.6 mM quadruplex DNA, 0.6 mM ligand, 0.4% PEG 2000 (w/v), 100mM potassium chloride, 100mM sodium chloride, 100mM lithium sulphate, 20mM potassium cacodylate, equilibrated against a reservoir well solution of 60% PEG 2000 (w/v), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.753 α = 90 b = 54.786 β = 90 c = 33.43 γ = 90
Symmetry Space Group C 2 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 105 CCD ADSC QUANTUM 315r 2010-10-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.90740, 0.92060, 0.92110 Diamond I03
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 2.254 21.188 98.2 0.034 24.9 3.8 2020 2020
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.38 91.5 0.095 0.095 8.1 2.6 271
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1K8P 2.4 15 1687 1687 77 99.06 0.2142 0.2132 0.2152 0.2343 0.2511 RANDOM 35.2997
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] -0.25 0.84 -0.58
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.31 r_scbond_it 2.847 r_angle_refined_deg 1.559 r_chiral_restr 0.056 r_gen_planes_refined 0.023 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 231 Solvent Atoms 27 Heterogen Atoms 48
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection SHELXD phasing