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KLHDC2 ubiquitin ligase in complex with USP1 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, 12.5% v/v MPD, 12.5% PEG1000, 12.5% w/v PEG3350, pH 6.5.
Crystal Properties Matthews coefficient Solvent content 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.496 α = 90 b = 87.086 β = 104.56 c = 88.322 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 2017-11-30 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 98 0.119 0.13 0.053 6.6 5.9 32634 32.82
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 80.3 0.527 0.604 0.287 0.714 3.8
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 2.5 43.067 1.38 22666 1399 99.99 0.2029 0.1996 0.2067 0.2525 0.2557 32.64
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 14.003 f_angle_d 1.303 f_chiral_restr 0.077 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5095 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction