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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide
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 0.5 M (NH4)H2PO4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.966 α = 90 b = 59.015 β = 90 c = 88.651 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 2018-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 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 1.718 37.23 99.6 0.074 1 19.8 12.73 32513
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 1.72 1.82 99.4 1.749 0.632 1.34 12.46
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 FOURIER SYNTHESIS THROUGHOUT 4V2Y 1.72 37.23 30878 1635 99.83 0.196 0.19459 0.2048 0.22261 0.2275 RANDOM 37.924
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] -0.35 0.93 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_4_deg 9.929 r_dihedral_angle_1_deg 7.351 r_long_range_B_refined 6.625 r_long_range_B_other 6.623 r_scangle_other 3.74 r_mcangle_it 2.485 r_mcangle_other 2.484 r_scbond_it 2.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_4_deg 9.929 r_dihedral_angle_1_deg 7.351 r_long_range_B_refined 6.625 r_long_range_B_other 6.623 r_scangle_other 3.74 r_mcangle_it 2.485 r_mcangle_other 2.484 r_scbond_it 2.439 r_scbond_other 2.438 r_angle_refined_deg 1.753 r_mcbond_it 1.663 r_mcbond_other 1.662 r_angle_other_deg 1.405 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 2221 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling