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ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 4 M sodium formate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.03 α = 90 b = 78.03 β = 90 c = 70.452 γ = 120
Symmetry Space Group P 62 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 2020-07-17 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 1.744 48.77 97.24 0.08357 0.08558 0.01818 1 32.13 21.4 13080 31.87
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 1.744 1.806 90.92 2.158 2.212 0.4767 0.65 1.37 20.5
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 SAD FREE R-VALUE 1.744 48.77 1.35 13069 2412 97.56 0.2392 0.235 0.24 0.2786 0.2835 49.73
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 23.2531 f_angle_d 1.7306 f_chiral_restr 0.1161 f_bond_d 0.0196 f_plane_restr 0.0112
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 461 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing