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Pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 296 Potassium Cacodylate, Lithium Sulfate, Magnesium Sulfate, Iso-propanol
Crystal Properties Matthews coefficient Solvent content 1.93 36.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.25 α = 90 b = 41.25 β = 90 c = 68.6 γ = 90
Symmetry Space Group P 41 21 2
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 2M 2016-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0000 ELETTRA 5.2R
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 1.7 35.35 99.1 0.078 0.081 0.99 21.74 22.9 6173 32.91
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 1.7 1.74 96.35 0.32 0.33 0.99 3.54 20
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CDB 1.7 35.35 6173 702 99.06 0.2684 0.2657 0.2935 0.2944 RANDOM 32.915
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] 1.39 1.39 -2.79
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.836 r_angle_other_deg 1.46 r_chiral_restr 0.064 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 493 Solvent Atoms 24 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction