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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Imidazolidine-2,4-dione (Hydantoin)
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, SITTING DROP 294 0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
Crystal Properties Matthews coefficient Solvent content 1.8 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.43 α = 90 b = 58.47 β = 90 c = 87.12 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 2011-09-09 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) 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 1.85 36.8 97.8 0.06 12.6 2.92 24990
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 94.6 0.6 1.86 2.87
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 1.85 34.96 23726 1261 98.59 0.16447 0.16243 0.1713 0.20283 0.2115 RANDOM 33.831
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] -0.59 -0.75 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.05 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 13.08 r_long_range_B_other 11.01 r_long_range_B_refined 11.001 r_scangle_other 9.366 r_scbond_it 7.367 r_scbond_other 7.364 r_dihedral_angle_1_deg 6.543 r_mcangle_it 6.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.05 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 13.08 r_long_range_B_other 11.01 r_long_range_B_refined 11.001 r_scangle_other 9.366 r_scbond_it 7.367 r_scbond_other 7.364 r_dihedral_angle_1_deg 6.543 r_mcangle_it 6.244 r_mcangle_other 6.242 r_mcbond_other 5.092 r_mcbond_it 5.09 r_angle_refined_deg 1.87 r_angle_other_deg 1.278 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 2265 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling