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Cereblon in complex with DDB1, CC-885, and GSPT1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TZ4 4TZ4, 3E1Y experimental model PDB 3E1Y 4TZ4, 3E1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280 200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.89 68.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.747 α = 90 b = 111.522 β = 95.81 c = 175.057 γ = 90
Symmetry Space Group P 1 2 1
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 ADSC QUANTUM 315r 2015-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 3.6 50 94.6 0.198 10.6 4.8 66582
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 3.6 3.66 93.9 0.796 2.1 3343
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4TZ4, 3E1Y 3.6 50 62827 3289 94.4 0.226 0.224 0.2251 0.273 0.2714 RANDOM 112.3
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] 2.62 1.25 -8.14 5.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.516 r_dihedral_angle_3_deg 24.831 r_dihedral_angle_4_deg 22.38 r_long_range_B_refined 22.277 r_long_range_B_other 22.277 r_mcangle_it 14.634 r_mcangle_other 14.634 r_scangle_other 14.429 r_dihedral_angle_1_deg 12.88 r_mcbond_it 9.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.516 r_dihedral_angle_3_deg 24.831 r_dihedral_angle_4_deg 22.38 r_long_range_B_refined 22.277 r_long_range_B_other 22.277 r_mcangle_it 14.634 r_mcangle_other 14.634 r_scangle_other 14.429 r_dihedral_angle_1_deg 12.88 r_mcbond_it 9.514 r_mcbond_other 9.512 r_scbond_it 9.217 r_scbond_other 9.214 r_angle_refined_deg 1.796 r_angle_other_deg 1.012 r_chiral_restr 0.146 r_bond_refined_d 0.017 r_gen_planes_refined 0.017 r_gen_planes_other 0.008 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25025 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing