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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a
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 1.8 31.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.656 α = 90 b = 59.02 β = 90 c = 88.593 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 1.5 49.12 99.5 0.11 1 14.29 12.6 48555
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 1.5 1.59 97.2 0.79 0.87 2.32 12.6
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 1.5 49.12 46128 2427 99.52 0.19463 0.19354 0.1933 0.21537 0.2153 RANDOM 24.005
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] -0.31 0.78 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 13.651 r_dihedral_angle_3_deg 12.755 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 4.832 r_long_range_B_other 4.81 r_scangle_other 1.825 r_angle_refined_deg 1.81 r_mcangle_it 1.779 r_mcangle_other 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 13.651 r_dihedral_angle_3_deg 12.755 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 4.832 r_long_range_B_other 4.81 r_scangle_other 1.825 r_angle_refined_deg 1.81 r_mcangle_it 1.779 r_mcangle_other 1.779 r_scbond_it 1.085 r_scbond_other 1.084 r_angle_other_deg 1.015 r_mcbond_it 1.01 r_mcbond_other 1.009 r_chiral_restr 0.106 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 2540 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling