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W-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZG8 Apo form ZZ-domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 400
Tris base/ Hydrochloric acid pH 8.5
Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 4.42 72.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.26 α = 90 b = 106.26 β = 90 c = 97.063 γ = 90
Symmetry Space Group I 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 EIGER X 16M 2022-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.28 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.785 40.77 99.56 0.1262 0.1287 0.02445 0.997 18.48 28.8 7204 129.65
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 2.785 2.884 2.093 2.131 0.3918 0.643 1.02
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 FREE R-VALUE 8ZG8 2.785 40.77 1.36 7204 1325 99.57 0.2373 0.2345 0.2432 0.2613 0.2612 143.49
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 23.9525 f_angle_d 0.9448 f_chiral_restr 0.0553 f_bond_d 0.0077 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1050 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing