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Crystal Structure of Nanobody VHH219 Bound to Its Antigen PA14 Cif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KD2 3KD2, 8E1C experimental model PDB 8E1C 3KD2, 8E1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 292.8 14.5% (w/v) PEG3350, 375 mM sodium malonate pH 4, 5 mM cobalt (II) chloride
Crystal Properties Matthews coefficient Solvent content 2.18 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.204 α = 90 b = 162.599 β = 95.36 c = 106.255 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 EIGER X 16M 2021-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979261 NSLS-II 17-ID-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 2.4 43.75 99.55 0.07373 0.08721 0.04621 0.998 11.64 3.5 99962 55.22
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 2.4 2.486 99.89 1.108 1.309 0.6915 0.501 1.25 3.5
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 3KD2, 8E1C 2.4 43.75 1.36 99942 5000 99.57 0.1967 0.1951 0.1956 0.2274 0.2279 69.39
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 21.6788 f_angle_d 1.0002 f_chiral_restr 0.0585 f_plane_restr 0.0097 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19052 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building PHENIX refinement