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Crystal Structure of Nanobody VHH113 Bound to Its Antigen PA14 Cif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KD2 experimental model Preliminary model of 8E1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 292.8 200 mM potassium bromide, 200 mM potassium thiocyanate, 100 mM sodium acetate pH 5, 3% (w/v) gamma-PGA (Na+ form, LM), 10% (w/v) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.83 56.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.185 α = 90 b = 185.941 β = 90 c = 106.753 γ = 90
Symmetry Space Group C 2 2 21
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 2018-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979339 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 1.7 46.49 99.06 0.1067 0.1158 0.04459 0.998 11.8 6.7 124313 26.22
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 1.7 1.761 98.74 1.646 1.788 0.6909 0.439 1.26 6.6
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 3KD2, 8E1C 1.7 46.49 1.33 124297 6228 99.07 0.1772 0.1761 0.176 0.1988 0.1987 29.61
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 12.8677 f_angle_d 0.8389 f_chiral_restr 0.0546 f_plane_restr 0.008 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6527 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building