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Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZVD 1ZVD and Swiss Model of Ubiquitin Variant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.5 M Ammonium Sulphate and 100 mM MES pH 6.0. Trypsin was added to the protein complex at a final concentration of 10 microgram per mL
Crystal Properties Matthews coefficient Solvent content 3.11 60.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.53 α = 90 b = 72.068 β = 94.607 c = 48.813 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M Mirrors 2020-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.45 67.83 97.1 0.089 0.982 8.8 3.3 24895 54.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 99.2 0.675 0.478 2.2 3.5
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 1ZVD and Swiss Model of Ubiquitin Variant 2.5 67.83 1.35 24076 1201 99.02 0.2045 0.2029 0.2033 0.2349 0.2373 70.6
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 24.5852 f_angle_d 1.1444 f_chiral_restr 0.0635 f_bond_d 0.0088 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3615 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing