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Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 283 Potassium cacodylate, Potassium chloride, Sodium cacodylate, MPD
Crystal Properties Matthews coefficient Solvent content 2.29 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.856 α = 90 b = 23.647 β = 107.59 c = 31.052 γ = 90
Symmetry Space Group P 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 100 PIXEL DECTRIS PILATUS 12M 2018-06-27 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 12M 2018-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 1.7712 Diamond I23 2 SYNCHROTRON DIAMOND BEAMLINE I23 3.3509 Diamond I23
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 1.74 29.6 99.5 0.021 1 15.6 6.24 4377
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 1.74 1.8 98.6 0.34 0.842 1.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD THROUGHOUT 1.74 29.6 4142 236 99.7 0.2418 0.2393 0.2438 0.2914 0.2986 RANDOM 42.481
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] -1.47 0.38 -1.47 2.24
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.403 r_angle_other_deg 1.379 r_chiral_restr 0.105 r_gen_planes_refined 0.012 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 303 Solvent Atoms 11 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling Aimless data scaling HKL2Map phasing