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Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab "NabFab"
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JB9 6JB9, 5C8J experimental model PDB 5C8J 6JB9, 5C8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 292 0.02 M Citric acid, 0.08 M BIS-TRIS propane, 16 % (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.92 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.53 α = 90 b = 130.28 β = 107.99 c = 223.98 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 EIGER2 X 16M 3.3 Undulator (Undulator A) 2021-06-11 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) 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 3.19 111.43 99.4 0.17 0.98 9.5 5.7 102005
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.19 3.36 0.737 0.47 1.9 5.4
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 THROUGHOUT 6JB9, 5C8J 3.19 90.907 0.31 99658 5099 96.98 0.2185 0.2159 0.2165 0.2671 0.2648 77.104
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37922 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 354
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction