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Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB
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, HANGING DROP 7.5 298 10% (w/v) PEG 8000, 0.1 M Tris-HCl (pH 7.5) and 0.1 M MgCl2
Crystal Properties Matthews coefficient Solvent content 3.75 67.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.459 α = 90 b = 99.459 β = 90 c = 148.426 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-F 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9750 Diamond I04
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 3.5 49.73 92.6 0.16 0.194 0.109 0.984 4.5 2.6 19211
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 3.5 3.83 88.4 0.694 0.849 0.48 0.543 2.6
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 3.5 49.73 18245 940 92.64 0.2208 0.2195 0.2231 0.2468 0.2541 RANDOM 105.444
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] -0.12 -0.06 -0.12 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.659 r_dihedral_angle_4_deg 13.438 r_dihedral_angle_3_deg 11.367 r_dihedral_angle_1_deg 4.916 r_angle_refined_deg 0.729 r_angle_other_deg 0.634 r_chiral_restr 0.028 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.659 r_dihedral_angle_4_deg 13.438 r_dihedral_angle_3_deg 11.367 r_dihedral_angle_1_deg 4.916 r_angle_refined_deg 0.729 r_angle_other_deg 0.634 r_chiral_restr 0.028 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7208 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 154
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing