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Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.46 α = 103.62 b = 47.74 β = 94.66 c = 100.35 γ = 98.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS3 6M 2018-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.99 46.66 91.4 0.048 12.6 3.7 52695
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 1.99 2.04 0.53 0.771 3.7
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 1.99 46.66 48292 2487 88.05 0.20394 0.20171 0.2084 0.24791 0.252 RANDOM 42.831
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] -1.19 -0.13 -1.33 2.57 -0.1 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.486 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 14.089 r_dihedral_angle_1_deg 6.67 r_long_range_B_refined 4.5 r_long_range_B_other 4.5 r_angle_refined_deg 1.224 r_angle_other_deg 1.087 r_mcangle_it 0.805 r_mcangle_other 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.486 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 14.089 r_dihedral_angle_1_deg 6.67 r_long_range_B_refined 4.5 r_long_range_B_other 4.5 r_angle_refined_deg 1.224 r_angle_other_deg 1.087 r_mcangle_it 0.805 r_mcangle_other 0.805 r_scangle_other 0.791 r_mcbond_it 0.47 r_mcbond_other 0.47 r_scbond_it 0.467 r_scbond_other 0.467 r_chiral_restr 0.044 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 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 5467 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing