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Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (WO2020264398 Ex23)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 9 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.04 α = 90 b = 73.594 β = 90 c = 93.973 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 2021-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.001 19.802 85.7 0.082 0.089 0.036 10.3 6.3 23434
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.001 2.126 26.3 1.339 1.456 0.566 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.001 19.8 23419 1139 85.7 0.2229 0.2216 0.2121 0.248 0.2416 RANDOM 48.96
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] -1.0204 -1.316 2.3363
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.79 t_omega_torsion 2.82 t_angle_deg 0.88 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 16.79 t_omega_torsion 2.82 t_angle_deg 0.88 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 3091 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 42
Software Software Software Name Purpose BUSTER refinement STARANISO data scaling XDS data reduction AMoRE phasing