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Crystal structure of Cbl-b bound to compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M HEPES pH7.5, 8% EG, 10% PEG8,000
Crystal Properties Matthews coefficient Solvent content 2.41 48.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.655 α = 90 b = 102.781 β = 90.246 c = 74.647 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 EIGER X 16M 2022-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.987 SSRF BL17U
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 1.95 49.665 98.5 0.075 0.996 10.3 3.4 61298
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.656
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 49.665 61272 2954 98.427 0.176 0.1739 0.183 0.2256 0.2333 32.32
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] 0.015 -0.262 1.151 -1.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.077 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 15.353 r_lrange_it 7.072 r_lrange_other 7.041 r_dihedral_angle_1_deg 6.138 r_scangle_it 5.186 r_scangle_other 5.185 r_mcangle_other 3.766 r_mcangle_it 3.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.077 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 15.353 r_lrange_it 7.072 r_lrange_other 7.041 r_dihedral_angle_1_deg 6.138 r_scangle_it 5.186 r_scangle_other 5.185 r_mcangle_other 3.766 r_mcangle_it 3.765 r_scbond_it 3.369 r_scbond_other 3.369 r_mcbond_it 2.546 r_mcbond_other 2.544 r_angle_refined_deg 1.746 r_angle_other_deg 1.314 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.19 r_symmetry_nbd_other 0.176 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.161 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6249 Nucleic Acid Atoms Solvent Atoms 594 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing