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Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OUO experimental model PDB 8RQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.81 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.882 α = 96.44 b = 52.638 β = 91.49 c = 130.348 γ = 99.22
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 EIGER X 9M 2023-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 2.91 46.1 97.8 0.99 3.3 6.6 20285
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 2.91 2.96 75.6 0.26 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.91 43.27 1.96 20285 1620 80.95 0.2524 0.2488 0.2508 0.2926 0.2913 74.17
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 14.9995 f_angle_d 0.8951 f_chiral_restr 0.0557 f_bond_d 0.0061 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6231 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 122
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2.multiplex data scaling PHASER phasing