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KLHDC2 ubiquitin ligase in complex with SelS C-end degron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 0.03M MgCl2*6H2O, 0.03M CaCl2*2H2O, 0.05M Imidazole, 0.05M MES monohydrate, 13.25% v/v MPD, 13.25% PEG1000, 13.25% w/v PEG3350, pH 6.8.
Crystal Properties Matthews coefficient Solvent content 2.04 39.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.637 α = 90 b = 88.596 β = 104.77 c = 88.824 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2017-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 50 99.3 0.138 0.156 0.073 5.9 4.5 33761 26.88
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 2.2 2.24 93 0.592 0.702 0.369 0.665 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 2VPJ 2.2 39.37 1.36 33734 2001 98.95 0.1697 0.1669 0.1692 0.216 0.2176 27.4218
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 19.603 f_angle_d 0.894 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5133 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction