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Homopurine parallel G-quadruplex from human chromosome 7 stabilized by K+ ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285.15 The well condition included 0.012 M NaCl, 0.08-0.1 M KCl, 0.04 M sodium cacodylate pH 5.5, 45% MPD, and 0.002 M hexammine cobalt(III) chloride
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.053 α = 90 b = 47.474 β = 90 c = 119.597 γ = 90
Symmetry Space Group F 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 196 PIXEL DECTRIS EIGER X 16M 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.98 30.44 99.2 0.049 0.054 0.023 0.999 15.1 5.8 4296 64.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 99.8 0.894 0.351 0.7 6.3
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 4G0F 1.98 24.71 1.35 4254 425 98.09 0.2362 0.2314 0.2331 0.2789 0.2875 95.26
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 36.279 f_angle_d 1.9337 f_chiral_restr 0.0686 f_bond_d 0.0142 f_plane_restr 0.0128
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 435 Solvent Atoms 4 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement Aimless data scaling Coot model building PHENIX phasing XDS data reduction