☰ Navigation Tabs
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2s
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 3mM thalidomide
Crystal Properties Matthews coefficient Solvent content 1.8 31.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.47 α = 90 b = 60.042 β = 90 c = 88.178 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 S 16M 2024-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.92 19.69 96.4 0.996 9.3 12.56 22809 44.089
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 1.92 2.03 77.9 0.526 1.22 13.33
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 1.92 19.69 21669 1140 96.35 0.19272 0.19051 0.1977 0.23532 0.2395 RANDOM 37.86
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] 1.11 -0.3 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.773 r_dihedral_angle_4_deg 17.521 r_dihedral_angle_3_deg 13.587 r_dihedral_angle_1_deg 7.212 r_long_range_B_refined 4.698 r_long_range_B_other 4.688 r_scangle_other 2.963 r_mcangle_it 2.455 r_mcangle_other 2.454 r_scbond_it 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.773 r_dihedral_angle_4_deg 17.521 r_dihedral_angle_3_deg 13.587 r_dihedral_angle_1_deg 7.212 r_long_range_B_refined 4.698 r_long_range_B_other 4.688 r_scangle_other 2.963 r_mcangle_it 2.455 r_mcangle_other 2.454 r_scbond_it 1.956 r_scbond_other 1.883 r_angle_refined_deg 1.74 r_angle_other_deg 1.63 r_mcbond_it 1.527 r_mcbond_other 1.527 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 2369 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building