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Ternary complex between VCB, BRD4-BD1 and PROTAC 48
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NW1 5nw1, 3mxf experimental model PDB 3MXF 5nw1, 3mxf
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1.4M Ammonium Sulfate, 4% (w/v) glycerol, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.26 62.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.031 α = 90 b = 79.031 β = 90 c = 204.206 γ = 120
Symmetry Space Group P 31 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 6M 2022-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.718 68.443 95.9 0.076 0.081 0.026 0.999 15.2 9.4 63052
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.718 1.871 69.1 1.399 1.481 0.483 0.621 9.3
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 5nw1, 3mxf 1.72 68.44 59918 3134 79.12 0.1692 0.1677 0.1773 0.1973 0.1993 RANDOM 37.641
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] -0.04 -0.02 -0.04 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.514 r_dihedral_angle_4_deg 22.487 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.827 r_angle_refined_deg 1.824 r_angle_other_deg 1.463 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.514 r_dihedral_angle_4_deg 22.487 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.827 r_angle_refined_deg 1.824 r_angle_other_deg 1.463 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3763 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 115
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing