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Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ 1UBQ, 5VNW experimental model PDB 5VNW 1UBQ, 5VNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277.15 0.1 M Bis-Tris pH 7.2
0.28 M MgCl2
21% PEG3350
0.15 M NaCl
0.05 M Tris/HCl pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.389 α = 90 b = 97.615 β = 109.959 c = 74.967 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 2M 2020-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.274 200 85.3 0.099 0.992 8 4 79157 1.2 18.58
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 1.55 1.659 34 0.296 2.6
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 1UBQ, 5VNW 1.55 35.95 1.33 79092 3986 74.31 0.1764 0.1745 0.1742 0.212 0.2125 25.86
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 13.7177 f_angle_d 0.9152 f_chiral_restr 0.058 f_plane_restr 0.008 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5275 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction MxCuBE data collection XDS data scaling PHASER phasing