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Crystal structure of pVHL:ElonginC:ElonginB complex bound to PROTAC JW48
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model 1vcb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 18% PEG 3350, HEPES pH7
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.797 α = 90 b = 60.787 β = 100.58 c = 97.228 γ = 90
Symmetry Space Group C 1 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 2M-F 2021-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999987 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 48.833 99.1 0.111 0.121 0.046 0.997 9.9 7 18781
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.8 1.207 1.299 0.477 0.752 7.3
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 2.3 47.833 18775 921 98.909 0.225 0.2226 0.2251 0.2612 0.2668 57.148
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] -2.992 -0.233 -0.663 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.6 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.136 r_lrange_it 3.21 r_lrange_other 3.209 r_dihedral_angle_2_deg 2.95 r_mcangle_it 1.867 r_mcangle_other 1.867 r_scangle_it 1.861 r_scangle_other 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.6 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.136 r_lrange_it 3.21 r_lrange_other 3.209 r_dihedral_angle_2_deg 2.95 r_mcangle_it 1.867 r_mcangle_other 1.867 r_scangle_it 1.861 r_scangle_other 1.86 r_mcbond_it 1.082 r_mcbond_other 1.081 r_scbond_it 1.079 r_scbond_other 1.079 r_angle_refined_deg 0.756 r_angle_other_deg 0.277 r_symmetry_xyhbond_nbd_refined 0.204 r_nbd_refined 0.181 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.144 r_nbd_other 0.099 r_symmetry_nbtor_other 0.075 r_symmetry_nbd_refined 0.069 r_chiral_restr 0.037 r_chiral_restr_other 0.019 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2704 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction