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Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other DDB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100mM HEPES pH 7.5, 18% PEG 10K
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.862 α = 90 b = 129.117 β = 90 c = 198.677 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 CCD MARMOSAIC 300 mm CCD 2014-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.00 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.01 50 98.5 0.181 5.9 6.1 37313
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.12 85.8 0.723 5.8 3184
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT DDB1 3.01 50 37253 1857 99.4 0.2049 0.2015 0.2706 0.2661 RANDOM 30.294
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] -1.52 1.67 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.812 r_dihedral_angle_4_deg 21.184 r_dihedral_angle_3_deg 19.871 r_dihedral_angle_1_deg 7.382 r_angle_refined_deg 1.211 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11043 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction PDB_EXTRACT data extraction Coot model building