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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7f
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 1.79 31.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.871 α = 90 b = 58.547 β = 90 c = 88.283 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 2018-04-18 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 1.65 48.79 99.9 0.07 1 20.72 12.9 36299
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) 1.65 1.75 99.6 0.82 0.87 2.35 13.2
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 1.65 48.79 34483 1816 99.88 0.19907 0.19777 0.2071 0.22371 0.2287 RANDOM 32.789
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] -0.15 0.71 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_3_deg 12.315 r_dihedral_angle_4_deg 11.374 r_dihedral_angle_1_deg 5.942 r_long_range_B_refined 5.175 r_long_range_B_other 5.054 r_scangle_other 1.828 r_angle_refined_deg 1.713 r_mcangle_it 1.463 r_mcangle_other 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_3_deg 12.315 r_dihedral_angle_4_deg 11.374 r_dihedral_angle_1_deg 5.942 r_long_range_B_refined 5.175 r_long_range_B_other 5.054 r_scangle_other 1.828 r_angle_refined_deg 1.713 r_mcangle_it 1.463 r_mcangle_other 1.462 r_scbond_it 1.153 r_scbond_other 1.153 r_angle_other_deg 0.971 r_mcbond_it 0.875 r_mcbond_other 0.875 r_chiral_restr 0.104 r_bond_refined_d 0.011 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 2198 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling