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Strcture of Nanobody (NB) specific to Interleukin-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Model generate dusing Rosetta software where CDR grafted from an antibody on to a nanobody scaffold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.29 62.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.397 α = 90 b = 157.397 β = 90 c = 105.253 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 270 2024-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.86 29.75 99.97 0.329 0.334 0.054 14.6 38 18171
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.97 99.66 4.458 4.458 4.526 0.771 1 33.89
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.86 29.75 1.33 18105 1666 99.63 0.2355 0.233 0.2327 0.2847 0.2856 86.83
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 15.8402 f_angle_d 0.6789 f_chiral_restr 0.0395 f_plane_restr 0.0047 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3488 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing