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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8i
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 1.75 29.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.385 α = 90 b = 59.297 β = 90 c = 86.209 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 2023-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0001 SLS X10SA
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 48.86 100 0.103 0.999 10.65 7.02 37772 48.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 99.9 1.572 0.512 1.11 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 48.86 19158 1012 99.92 0.20883 0.20659 0.2126 0.25337 0.2588 RANDOM 46.774
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] -0.38 -2.77 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.265 r_dihedral_angle_3_deg 11.654 r_dihedral_angle_4_deg 11.16 r_dihedral_angle_1_deg 6.971 r_long_range_B_refined 4.39 r_long_range_B_other 4.384 r_scangle_other 2.361 r_mcangle_it 1.89 r_mcangle_other 1.89 r_scbond_it 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.265 r_dihedral_angle_3_deg 11.654 r_dihedral_angle_4_deg 11.16 r_dihedral_angle_1_deg 6.971 r_long_range_B_refined 4.39 r_long_range_B_other 4.384 r_scangle_other 2.361 r_mcangle_it 1.89 r_mcangle_other 1.89 r_scbond_it 1.513 r_scbond_other 1.47 r_angle_refined_deg 1.413 r_angle_other_deg 1.228 r_mcbond_it 1.148 r_mcbond_other 1.148 r_chiral_restr 0.054 r_bond_refined_d 0.006 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 1994 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building