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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one (Butyrolactam)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V2Y
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 = 56.911 α = 90 b = 59.686 β = 90 c = 88.443 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 2015-03-08 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 1.9 37.4 98.4 0.05 1 12.5 2.86 24410
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 1.9 2.01 96.7 0.49 0.79 1.89 2.81
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 2V2Y 1.9 37.4 23182 1218 99.41 0.1789 0.17654 0.1861 0.22474 0.2281 RANDOM 41.434
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] 0.32 1.2 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.952 r_dihedral_angle_4_deg 16.964 r_dihedral_angle_3_deg 13.701 r_long_range_B_refined 6.113 r_long_range_B_other 6.065 r_dihedral_angle_1_deg 6.056 r_scangle_other 3.281 r_mcangle_it 2.225 r_mcangle_other 2.224 r_scbond_it 2.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.952 r_dihedral_angle_4_deg 16.964 r_dihedral_angle_3_deg 13.701 r_long_range_B_refined 6.113 r_long_range_B_other 6.065 r_dihedral_angle_1_deg 6.056 r_scangle_other 3.281 r_mcangle_it 2.225 r_mcangle_other 2.224 r_scbond_it 2.082 r_scbond_other 2.081 r_angle_refined_deg 1.537 r_mcbond_other 1.435 r_mcbond_it 1.434 r_angle_other_deg 1.411 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 2439 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling