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Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M Imidazole, 0.1 M MES monohydrate pH 6.5
0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09M Ammonium sulfate
12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.937 α = 90 b = 76.093 β = 90 c = 105.464 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 EIGER2 X 16M 2023-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.81 50 98.6 0.064 0.997 36 10.9 35624
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 1.81 1.84 98.3 0.94 0.827 9.9
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 1.81 43.68 33780 1795 98.34 0.19669 0.19491 0.2024 0.22962 0.2377 RANDOM 32.702
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] -1.2 2.69 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 18.081 r_dihedral_angle_3_deg 13.882 r_long_range_B_other 6.621 r_long_range_B_refined 6.615 r_dihedral_angle_1_deg 6.471 r_scangle_other 4.973 r_mcangle_other 4.148 r_mcangle_it 4.147 r_scbond_it 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 18.081 r_dihedral_angle_3_deg 13.882 r_long_range_B_other 6.621 r_long_range_B_refined 6.615 r_dihedral_angle_1_deg 6.471 r_scangle_other 4.973 r_mcangle_other 4.148 r_mcangle_it 4.147 r_scbond_it 3.35 r_scbond_other 3.329 r_mcbond_it 3.053 r_mcbond_other 3.039 r_angle_refined_deg 1.451 r_angle_other_deg 1.334 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2966 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 51
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement HKL-3000 data reduction PHASER phasing