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T-Motif1-Motif2 right-left hybrid parallel G-quadruplex in complex with N-methylmesoporphyrin IX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9CIY right-left hybrid G-quadruplex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 285 008 M potassium chloride, 0.02 M magnesium chloride hexahydrate, 0.04 M sodium cacodylate trihydrate pH 6.0, 45% MPD, 12 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.07 40.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.572 α = 90 b = 57.042 β = 90 c = 57.641 γ = 90
Symmetry Space Group P 2 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 196 PIXEL DECTRIS PILATUS 6M-F 2023-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.34 57.64 99.3 0.075 0.998 14.2 6 3310 77.34
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 2.34 2.42 2.279 0.469 0.6
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 2.34 40.54 1.34 3232 165 97.82 0.2101 0.2075 0.2102 0.2569 0.2581
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 34.755 f_angle_d 1.61 f_chiral_restr 0.063 f_bond_d 0.012 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 569 Solvent Atoms Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHENIX phasing