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Cereblon in complex with SALL4 and (S)-thalidomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TZ4 4TZ4, 5YJ0 experimental model PDB 5YJ0 4TZ4, 5YJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.41 48.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.962 α = 90 b = 92.718 β = 90 c = 43.986 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 2M-F 2019-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 43.99 100 0.158 0.044 0.997 12 12.9 11808 24.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 1.31 0.363 0.826 2.5 12.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4TZ4, 5YJ0 1.9 34.674 1.34 11790 561 99.95 0.1929 0.1908 0.1929 0.2358 0.237
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 7.452 f_angle_d 1.375 f_chiral_restr 0.046 f_bond_d 0.011 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1050 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing