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Racemic crystal structure of a tetramolecular DNA G-quadruplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 352D PDB ENTRY 352D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 100 mM magnesium chloride hexahydrate, 1.7 M 1,6-hexanediol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.94 α = 103.34 b = 39 β = 103.37 c = 84.08 γ = 90.04
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K 2013-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.695 37.886 97.69 0.1643 1.7 1.7 12894 12597 2 2 49.77
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 2.695 2.79 97.34 0.4338 1.6 1.6 1292
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 352D 2.695 37.886 11237 11917 680 97.39 0.29544 0.29388 0.2871 0.32532 0.3211 RANDOM 27.827
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] 0.01 0.03 -0.02 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.405 r_chiral_restr 0.097 r_gen_planes_refined 0.011 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1706 Solvent Atoms 1 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling