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Crystal structure of a four-tetrad, parallel, and Na+ stabilized Tetrahymena thermophila telomeric G-quadruplex in complex with N-methyl mesoporphyrin IX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Well condition contained 100 mM NaCl, 100 mM NaI, 100 mM NaF, 30% MPD, and 50 mM Na cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.93 34.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.284 α = 90 b = 34.716 β = 106.537 c = 34.397 γ = 90
Symmetry Space Group C 1 2 1
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 2021-02-12 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 32.97 96.2 0.118 0.14 0.075 0.987 9.5 3.3 3905 52.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 73.1 0.846 0.599 0.836 0.8 2.8
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 6W9P 1.99 32.97 1.37 3802 175 94.53 0.2418 0.241 0.2487 0.2532 0.2585 77.61
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 36.019 f_angle_d 1.3333 f_chiral_restr 0.0404 f_plane_restr 0.0056 f_bond_d 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 467 Solvent Atoms 12 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHENIX phasing