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E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.482 α = 90 b = 94.593 β = 97.45 c = 81.18 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 108 CCD ADSC QUANTUM 315 2020-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
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 2.56 94.6 99.1 0.99 12.2 6.9 22772 55.35
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 2.56 2.68 0.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6DC6 2.56 80.5 1.36 22689 1997 98.77 0.2156 0.2122 0.25 0.2226 66.25
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 15.5029 f_angle_d 0.7683 f_chiral_restr 0.059 f_bond_d 0.0057 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3915 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing