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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8b
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 1.81 32.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.536 α = 90 b = 59.8 β = 90 c = 88.01 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 2023-06-11 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 2.03 47.61 99.9 0.163 0.997 8.86 7.06 263076 43.893
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 2.03 2.15 99.7 1.849 0.529 1.03 7.24
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 2.03 47.61 18897 999 99.78 0.20724 0.20509 0.2113 0.24929 0.2539 RANDOM 41.255
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] -0.39 0.52 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.695 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_3_deg 13.023 r_dihedral_angle_1_deg 7.286 r_long_range_B_refined 4.133 r_long_range_B_other 4.13 r_scangle_other 2.169 r_mcangle_it 1.538 r_mcangle_other 1.538 r_angle_refined_deg 1.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.695 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_3_deg 13.023 r_dihedral_angle_1_deg 7.286 r_long_range_B_refined 4.133 r_long_range_B_other 4.13 r_scangle_other 2.169 r_mcangle_it 1.538 r_mcangle_other 1.538 r_angle_refined_deg 1.494 r_scbond_it 1.384 r_scbond_other 1.308 r_angle_other_deg 1.252 r_mcbond_it 0.933 r_mcbond_other 0.933 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 2280 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building