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KLHDC2 ubiquitin ligase in complex with a novel small-molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 0.03 M MgCl2*6H2O, 0.03 M CaCl2*2H2O, 10% (w/v) PEG 20000, 20% (v/v) PEG MME, 0.1 M Tris (base)/ bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.381 α = 90 b = 88.165 β = 104.39 c = 88.512 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 PIXEL DECTRIS EIGER2 S 9M 2023-06-22 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 1.44 44.08 70.05 0.064 0.076 0.041 2967.5 3.1 85458 25.45
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 1.44 2.071 99.48 0.1776 0.2113 0.1132 0.597 3.2 3.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 44.08 1.44 85458 2273 97.31 0.1671 0.1661 0.2018 0.1861 28.9
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 6.1796 f_angle_d 0.575 f_chiral_restr 0.0442 f_plane_restr 0.0036 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5184 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement DIALS data scaling PHENIX phasing Coot model building