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Four carbons pendant 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 Kcacodylate, Li2SO4, PEG400
Crystal Properties Matthews coefficient Solvent content 1.93 0.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.1 α = 90 b = 42.1 β = 90 c = 34.15 γ = 90
Symmetry Space Group P 42 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 PILATUS3 6M 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97264 ESRF ID30B
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 1.49 29.77 98.2 0.06 0.065 0.999 9.2 10.697 5252 51.743
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 1.49 1.58 93.9 0.453 6.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CDB 1.6 29.77 3925 418 99.25 0.2845 0.2816 0.2816 0.3099 0.31 RANDOM 78.865
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] 3.4 3.4 -6.79
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 1.819 r_angle_refined_deg 1.241 r_chiral_restr 0.087 r_gen_planes_refined 0.014 r_bond_refined_d 0.008 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 250 Solvent Atoms 2 Heterogen Atoms 66
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing