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Ternary complex between VCB, BRD4-BD1 and PROTAC 49
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 1.8M ammonium sulfate, 4% (w/v) glycerol, 0.1M bis-Tris pH5.5
Crystal Properties Matthews coefficient Solvent content 3 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.754 α = 90 b = 79.754 β = 90 c = 184.93 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 2022-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97626 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 3.18 64.7 85.4 0.353 0.363 0.084 0.995 9.4 18.3 9832
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 3.18 3.346 41.2 2.206 2.261 0.492 0.512 20.9
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 3.18 64.7 9370 462 81.66 0.2207 0.2179 0.2227 0.2739 0.2722 RANDOM 71.841
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] -0.23 -0.11 -0.23 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.211 r_dihedral_angle_2_deg 11.734 r_dihedral_angle_1_deg 4.8 r_angle_refined_deg 1.557 r_angle_other_deg 0.515 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3599 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction