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Crystal structure of (GGGTT)3GGG G-quadruplex in complex with small molecule ligand RHPS4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 sodium formate, PEG 20000, Bis-tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.31 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.162 α = 90 b = 62.667 β = 90 c = 256.675 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 183 PIXEL DECTRIS EIGER X 16M 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.47 128.34 97.8 0.121 0.136 0.971 6.6 4 21360 43.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.57 92.6 0.728 0.829 0.844 1.5 3.8
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 2.47 128.34 1.33 20879 1957 95.42 0.2968 0.2946 0.2943 0.3175 0.317 53.1
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 36.8993 f_angle_d 0.6103 f_chiral_restr 0.0235 f_bond_d 0.0045 f_plane_restr 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3810 Solvent Atoms 14 Heterogen Atoms 285
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX phasing XDS data reduction XDS data scaling