☰ Navigation Tabs
VCB in complex with VHL-binding compound 114
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 277 0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.07 40.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.095 α = 90 b = 94.095 β = 90 c = 365.561 γ = 90
Symmetry Space Group P 41 2 2
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 EIGER2 S 16M 2023-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 2.28 49.21 99.9 0.999 15.37 26.97 76014 63.802
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 2.28 2.42 99.7 0.866
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 2.28 49.21 1.33 75642 1588 99.68 0.2484 0.2472 0.2485 0.3012 0.3043 62.8
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 11.8531 f_angle_d 0.479 f_chiral_restr 0.0404 f_plane_restr 0.0036 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10517 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 148
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing