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Crystal structure of mouse pVHL-ElonginB-ElonginC complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20 mM Hepes, pH 7.5, 100 mM NaCl, 1 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.36855 48.10174
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.48 α = 90 b = 59.78 β = 100.85 c = 91.67 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 EIGER X 16M 2025-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
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 2.1 46.04 99.5 0.058 0.082 0.058 0.997 10.5 1.9 22839
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 2.1 2.16 0.559 0.791 0.559 0.55 1.3
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 (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 2.1 46.04 21696 1142 99.54 0.18447 0.18246 0.191 0.22172 0.2205 RANDOM 37.478
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] 0.98 -1.78 -1.22 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.661 r_dihedral_angle_2_deg 8.925 r_long_range_B_refined 7.826 r_long_range_B_other 7.81 r_dihedral_angle_1_deg 7.289 r_scangle_other 6.657 r_scbond_it 4.587 r_scbond_other 4.586 r_mcangle_it 4.164 r_mcangle_other 4.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.661 r_dihedral_angle_2_deg 8.925 r_long_range_B_refined 7.826 r_long_range_B_other 7.81 r_dihedral_angle_1_deg 7.289 r_scangle_other 6.657 r_scbond_it 4.587 r_scbond_other 4.586 r_mcangle_it 4.164 r_mcangle_other 4.163 r_mcbond_it 2.945 r_mcbond_other 2.936 r_angle_refined_deg 1.729 r_angle_other_deg 0.568 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2761 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing