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Non-canonical quadruplex containing the oxidation product 8-oxoguanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MF5 1MF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 291 2 ul 40 mM sodium cacodylate, 1 ul 80 mM hexammine (III) cobalt, 1 ul 10% MPD, 2 ul 800 mM potassium chloride, ul 30 mM sodium chloride, 2 ul 1 mM DNA
Crystal Properties Matthews coefficient Solvent content 1.73 28.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.035 α = 90 b = 58.846 β = 90 c = 45.488 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU HyPix-6000HE 2021-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.6 18.79 99.8 0.054 0.086 0.036 0.996 13.6 5 4151 6.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 0.958
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1MF5 1.6 18.79 1.39 4128 326 98.25 0.1866 0.1861 0.1983 0.1969 0.2071 15.07
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 f_dihedral_angle_d 31.3623 f_angle_d 2.0374 f_chiral_restr 0.0991 f_bond_d 0.0216 f_plane_restr 0.0119
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 282 Solvent Atoms 47 Heterogen Atoms 28
Software Software Software Name Purpose CrysalisPro data reduction CrysalisPro data scaling PHASER phasing Coot model building PHENIX refinement