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Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35
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 20% PEG 3350
0.18M tris amonium citrate
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.46 α = 90 b = 108.46 β = 90 c = 242.85 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-F 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000029 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 2.2 49.516 99.9 0.994 8.65 26.7427710681 74354 32.0006866889
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 2.2 2.26 0.444
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3KCI 2.20007772782 49.5160649028 1.34635839883 74258 3709 99.928678123 0.184693201749 0.182249275454 0.231046732051 0.2022 37.187308999
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 20.9804520664 f_angle_d 0.633893708813 f_chiral_restr 0.0495003936953 f_plane_restr 0.00342762737229 f_bond_d 0.00336706399674
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8436 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing