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Ternary complex between VCB, BRD4-BD2 and PROTAC 51
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M sodium malonate dibasic monohydrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.483 α = 90 b = 82.483 β = 90 c = 169.088 γ = 120
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 2022-02-04 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 2.7 65.8 91 0.081 0.089 0.039 0.999 12.3 5.3 29056
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 2.704 2.89 46.9 1.24 1.385 0.612 0.463 5.1
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 5t35 2.7 65.8 27542 1512 82.55 0.1905 0.1878 0.1914 0.2426 0.2443 RANDOM 85.034
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] -1.36 -0.68 -1.36 4.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.437 r_dihedral_angle_4_deg 19.699 r_dihedral_angle_3_deg 18.937 r_dihedral_angle_1_deg 6.967 r_angle_refined_deg 1.731 r_angle_other_deg 1.481 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.437 r_dihedral_angle_4_deg 19.699 r_dihedral_angle_3_deg 18.937 r_dihedral_angle_1_deg 6.967 r_angle_refined_deg 1.731 r_angle_other_deg 1.481 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7099 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 159
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing