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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product
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 294 0.4 M Ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 1.77 30.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.455 α = 90 b = 58.824 β = 90 c = 88.234 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 PILATUS 6M-F 2018-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 44.12 99.8 0.09 0.999 15.09 12.66 43510
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.64 98.9 0.98 0.85
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4v2y 1.55 44.12 41337 2173 99.78 0.18815 0.18685 0.1978 0.21293 0.2187 RANDOM 28.054
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] -0.47 0.99 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.472 r_dihedral_angle_3_deg 12.963 r_dihedral_angle_4_deg 12.044 r_dihedral_angle_1_deg 6.3 r_long_range_B_refined 4.507 r_long_range_B_other 4.507 r_scangle_other 2.231 r_mcangle_it 1.925 r_mcangle_other 1.924 r_angle_refined_deg 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.472 r_dihedral_angle_3_deg 12.963 r_dihedral_angle_4_deg 12.044 r_dihedral_angle_1_deg 6.3 r_long_range_B_refined 4.507 r_long_range_B_other 4.507 r_scangle_other 2.231 r_mcangle_it 1.925 r_mcangle_other 1.924 r_angle_refined_deg 1.78 r_scbond_it 1.364 r_scbond_other 1.364 r_mcbond_it 1.132 r_mcbond_other 1.131 r_angle_other_deg 1.017 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2516 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling