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Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FQD experimental model PDB 1AUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200
Crystal Properties Matthews coefficient Solvent content 1.94 36.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.176 α = 90 b = 81.213 β = 90 c = 99.02 γ = 90
Symmetry Space Group P 21 21 2
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 2024-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.61 74.24 96.5 0.153 0.997 10.9 11 30713
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 2.95 3.05 0.438
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 2.95 43.78 1.35 29668 1530 93.07 0.2329 0.2314 0.233 0.2603 0.2627 85.42
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 16.8356 f_angle_d 1.3216 f_chiral_restr 0.0824 f_bond_d 0.0107 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9998 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement DIALS data reduction XDS data scaling PHASER phasing