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Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 293.1500
hanging drop
20% PEG 3350
0.18M tris amonium citrate
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.952 α = 90 b = 108.952 β = 90 c = 243.16 γ = 90
Symmetry Space Group P 43 21 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 PILATUS 2M 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999882 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.01 48.725 99.2 0.968 5.81 5.91558595531 54825 58.2859737188
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.2 0.401
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 3KCI 3.01478056714 48.7248156569 1.34693515008 54780 2747 99.3200979059 0.201297269544 0.198473603185 0.1991 0.255047390534 0.2556 58.9796357813
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 7.31880543032 f_angle_d 1.09392565119 f_chiral_restr 0.0651248179727 f_bond_d 0.00939813958403 f_plane_restr 0.00547378181583
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8406 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing