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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2j
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
Crystal Properties Matthews coefficient Solvent content 1.78 30.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.507 α = 90 b = 59.361 β = 90 c = 88.337 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 EIGER2 X 16M 2024-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.74 50 99.8 0.999 14.31 6.96 58605 37.2
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 1.74 1.85 99.5 0.611 1.57 6.79
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.74 47.65 29479 1556 99.84 0.18549 0.18387 0.192 0.2171 0.2213 RANDOM 34.748
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] 1.55 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.996 r_dihedral_angle_4_deg 19.41 r_dihedral_angle_3_deg 12.589 r_dihedral_angle_1_deg 7.033 r_long_range_B_refined 4.552 r_long_range_B_other 4.537 r_scangle_other 2.576 r_mcangle_it 1.758 r_mcangle_other 1.758 r_scbond_it 1.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.996 r_dihedral_angle_4_deg 19.41 r_dihedral_angle_3_deg 12.589 r_dihedral_angle_1_deg 7.033 r_long_range_B_refined 4.552 r_long_range_B_other 4.537 r_scangle_other 2.576 r_mcangle_it 1.758 r_mcangle_other 1.758 r_scbond_it 1.664 r_scbond_other 1.637 r_angle_refined_deg 1.573 r_angle_other_deg 1.4 r_mcbond_it 1.09 r_mcbond_other 1.09 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2402 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building