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Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.57 293 30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.8 α = 90 b = 117.292 β = 97.3 c = 196.713 γ = 90
Symmetry Space Group P 1 21 1
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 2019-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.78 150.57 98.2 0.367 0.286 0.988 3.2 4.6 67972 82.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.78 3.86 87.6 1.813 1.439 0.28 0.7 4.5
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 5fqd 3.78 150.57 67299 3410 97.6 0.2895 0.2887 0.2749 0.3031 0.2925 RANDOM 124.3
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] -2.5162 0.5111 -3.1434 5.6596
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.27 t_omega_torsion 2.01 t_angle_deg 0.7 t_bond_d 0.004 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.27 t_omega_torsion 2.01 t_angle_deg 0.7 t_bond_d 0.004 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37402 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 148
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing