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Crystal structure of the non-canonical quadruplex d(GCATGCT) before soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 291 2 ul 40 mM sodium cacodylate, 1 ul 80 mM hexammine (III) cobalt, 1 ul 10% MPD, 2 ul 800 mM potassium chloride, ul 30 mM sodium chloride, 2 ul 1 mM DNA
Crystal Properties Matthews coefficient Solvent content 1.77 30.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.157 α = 90 b = 59.156 β = 90 c = 45.666 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER2 XE 16M 2019-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8266 Diamond I03
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 1.08 24.83 99.6 0.998 14 6 13221 9.25
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 1.08 1.1 0.893
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 1.08 24.83 1.41 13176 1169 98.96 0.1649 0.1638 0.1682 0.185 0.196 19.46
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 31.9165 f_angle_d 1.7074 f_chiral_restr 0.1317 f_plane_restr 0.0175 f_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 280 Solvent Atoms 50 Heterogen Atoms 42
Software Software Software Name Purpose GDA data collection xia2 data reduction DIALS data scaling PHENIX phasing PHENIX refinement Coot model building