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Structure of the DDB1-CRBN E3 ubiquitin ligase bound to lenalidomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DDB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE PH 6.2, 80 MM NAH2PO4, 120 MM K2HPO4, 950 MM TRI-NA CITRATE.
Crystal Properties Matthews coefficient Solvent content 3.18 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.11 α = 90 b = 172.11 β = 90 c = 139.84 γ = 120
Symmetry Space Group P 32 2 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 2M MIRRORS 2012-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 2.95 30 99.7 0.13 14.33 7.04 50544 -3 97.33
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 2.95 3.03 100 1.5 1.01 7.1
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 DDB1 2.95 29.71 50542 2528 99.85 0.1951 0.193 0.2067 0.2339 0.2458 RANDOM 95.31
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] 3.1998 3.1998 -6.3997
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.7 t_omega_torsion 2.69 t_angle_deg 1.18 t_bond_d 0.009 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 17.7 t_omega_torsion 2.69 t_angle_deg 1.18 t_bond_d 0.009 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 11411 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 20
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing