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NbE201 a nanobody binding human neutrophil elastase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The crystals were grown at 20oC using the sitting drop vapor diffusion method. The drop contained 0.2 uL of NbE201 at a concentration of 15 mg/mL-1 and 0.2 uL of PBS buffer pH 7.4, 10 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, in a cryo-protectant solution of 0.2 M Ca Acetate, 0. 1M Na Cacodylate pH 6.5 with 18% (%v/v) polyethylene glycol 8000 et 33% (%v/v) glycerol before being frozen in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.68 α = 90 b = 88.68 β = 90 c = 86.56 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER X 9M 2022-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 44.35 97.9 0.994 8.24 9.5 43692
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99 0.626
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 1.8 44.34 1 43692 4100 96.94 0.2188 0.2169 0.2184 0.2543 0.2556
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 10.999 f_angle_d 0.884 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3808 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing