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Crystal Structure of Nanobody VHH108 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 structure of 8E1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 292.8 Morpheus I Condition G2 (composition by Molecular Dimensions stock solutions with catalogue numbers listed at end)
20% (v/v) ethylene glycol, 10% (w/v) PEG8000, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM potassium sodium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM imidazole/MES monohydrate (acid) pH 6.5
Stock mixtures listed below with catalogue number in brackets.
30% (v/v) Precipitant Mix 2 [MD2-100-82], 100 mM carboxylic acids mix [MD2-100-76], 100 mM Buffer System 1 pH 6.5 [MD2-100-100]
Crystal Properties Matthews coefficient Solvent content 2.89 57.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.995 α = 90 b = 98.995 β = 90 c = 196.987 γ = 120
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 2020-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979312 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 2.3 44.23 99.26 0.08607 0.1034 0.05634 0.991 7.36 2.9 48028 49.93
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 2.3 2.382 99.79 0.7833 1.004 0.6205 0.425 1.28 2.4
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 3KD2, 8E1B 2.3 44.23 1.35 48020 2417 99.27 0.1827 0.1813 0.1825 0.2098 0.211 57.77
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 14.1238 f_angle_d 0.9768 f_chiral_restr 0.0595 f_bond_d 0.0091 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6554 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building