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Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other RING domain of TRIM2, Ubiquitin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.2 M sodium formate, 0.1 M bis-tris propane, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.12 α = 90 b = 69.27 β = 90 c = 151.87 γ = 90
Symmetry Space Group P 21 21 21
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 4M 2020-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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 2.295 40.92 97.52 0.993 14.54 12.7 32226 50.47
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 2.295 2.377 0.549
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 RING domain of TRIM2, Ubiquitin 2.4 40.92 32103 1606 99.78 0.215 0.2141 0.2236 0.2326 0.2409 50.47
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 17.187 f_angle_d 1.6783 f_chiral_restr 0.0837 f_bond_d 0.012 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4088 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction MxCuBE data collection PHENIX phasing Coot model building