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Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previous in house experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.16 α = 90 b = 129.518 β = 90 c = 198.797 γ = 90
Symmetry Space Group P 21 21 21
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 16M 2018-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.39 129.52 99.9 0.112 0.999 16.6 13.5 74800
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.44 97.8 1.228 0.828 2.1 12.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.39 99.4 1.37 74800 3696 99.85 0.197 0.1945 0.2164 0.2441 0.2517 RANDOM
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 6.676 f_angle_d 1.022 f_chiral_restr 0.059 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11787 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling