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Structure of the DDB1-CRBN E3 ubiquitin ligase bound to thalidomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DDB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE; 80 MM NAH2PO4; 120 MM K2HPO4; 800 MM TRI-NA CITRATE., pH 6
Crystal Properties Matthews coefficient Solvent content 3.18 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.18 α = 90 b = 172.18 β = 90 c = 140.09 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 6M MIRRORS 2012-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 2.98 30 99.9 0.12 15.77 7.9 49202 -3 97.97
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 2.98 3.06 99.9 1.37 1.22 5.6
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 2.98 29.82 49199 2460 99.97 0.1987 0.1969 0.2051 0.2332 0.239 RANDOM 87.64
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] 5.9433 5.9433 -11.8865
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.94 t_omega_torsion 2.53 t_angle_deg 1.11 t_bond_d 0.008 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 16.94 t_omega_torsion 2.53 t_angle_deg 1.11 t_bond_d 0.008 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 11405 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 20
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing