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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2p
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 1.76 30.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.831 α = 90 b = 59.8 β = 90 c = 86.868 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 CdTe 16M 2024-11-21 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) Rrim 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 2.35 50 100 0.132 0.997 9.51 6.9 23376 59.56
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 2.35 2.49 99.9 0.481 1.6 7.1
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 2.35 49.26 11989 627 99.95 0.24044 0.23838 0.2424 0.28066 0.2764 RANDOM 57.364
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] -2.98 -4.84 7.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.112 r_dihedral_angle_4_deg 16.693 r_dihedral_angle_3_deg 14.772 r_dihedral_angle_1_deg 7.214 r_long_range_B_refined 3.313 r_long_range_B_other 3.312 r_mcangle_it 1.716 r_mcangle_other 1.715 r_scangle_other 1.709 r_angle_refined_deg 1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.112 r_dihedral_angle_4_deg 16.693 r_dihedral_angle_3_deg 14.772 r_dihedral_angle_1_deg 7.214 r_long_range_B_refined 3.313 r_long_range_B_other 3.312 r_mcangle_it 1.716 r_mcangle_other 1.715 r_scangle_other 1.709 r_angle_refined_deg 1.406 r_angle_other_deg 1.234 r_scbond_it 1.025 r_scbond_other 1.024 r_mcbond_it 1.019 r_mcbond_other 1.019 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 2199 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data scaling Coot model building