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nanobody bound to Interleukin-2Rbeta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B5I 2b5i, 5lhr experimental model PDB 5LHR 2b5i, 5lhr
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 295 0.23 M ammonium sulfate, 0.08 M Bis Tris pH 5.5, 23% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.17 61.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.698 α = 99.566 b = 69.505 β = 99.854 c = 91.721 γ = 90.191
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 6M 2021-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.92 44.53 94.5 0.101 0.119 0.062 0.996 7.8 3.6 73848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 73 1.358 1.606 0.848 0.556 3.4
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 2b5i, 5lhr 1.93 44.53 1.96 73633 2007 95.94 0.2137 0.2127 0.2139 0.2471 0.2476 54.65
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 15.1726 f_angle_d 0.7033 f_chiral_restr 0.0457 f_plane_restr 0.0052 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5163 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 295
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction