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Hybrid G-quadruplex from Tetrahymena thermophila telomeric sequence in complex with TrisQO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XT7 Same DNA without ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M potassium chloride,
0.01 calcium chloride dihydrate,
0.05 M HEPES sodium pH 7.0,
10% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.913 α = 90 b = 54.913 β = 90 c = 98.701 γ = 120
Symmetry Space Group P 61 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 PILATUS 6M 2023-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.656 47.556 100 0.999 11.3 18.6 11080 32.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.656 1.684 100 4.554 0.572 15.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.66 27.46 1.34 11040 578 99.62 0.2149 0.2136 0.2175 0.2358 0.2394 49.2
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 31.975 f_angle_d 1.0975 f_chiral_restr 0.0569 f_bond_d 0.0088 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 531 Solvent Atoms 33 Heterogen Atoms 140
Software Software Software Name Purpose PHENIX refinement Coot model building autoPROC data reduction PHENIX phasing autoPROC data scaling