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Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.85 M sodium formate, 17.5% PEG 20000, 0.05 M Bis-Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.03 59.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.93 α = 90 b = 60.93 β = 90 c = 194.342 γ = 120
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 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 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 2.388 64.78 97.5 0.067 0.369 21.4 19 5748 90.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.388 2.473 86.9 0.369 0.6 19
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6P45 2.39 64.78 1.35 5748 567 97.48 0.2364 0.2352 0.2433 0.249 0.2672 Random selection 115.44
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 36.1424 f_angle_d 1.7606 f_chiral_restr 0.0421 f_bond_d 0.0086 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 707 Solvent Atoms Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building