☰ Navigation Tabs
Crystal structure of pVHL:EloB:EloC in complex with MP-1-39
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 NaCl, 0.1M HEPES pH 7.5, and 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.237 α = 81.41 b = 47.345 β = 76.78 c = 99.746 γ = 80.49
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 PILATUS3 6M 2022-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6702 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 40.02 95.1 0.976 15.7 3.6 48840 37.34
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 2.05 2.09 0.924
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 31.64 1.98 48785 2508 94.98 0.185 0.1833 0.1834 0.2163 0.2167 45.8
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.0818 f_angle_d 1.1259 f_chiral_restr 0.0662 f_bond_d 0.0136 f_plane_restr 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5301 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing