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Crystal structure of neutralizing Fab Eq4.Dp46-3D from equine antivenom bound to a consensus short chain three finger alpha-neurotoxin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z14 scNTx experimental model PDB 8R4N Fab heavy and Light
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 0.1M Tris HCl (pH 8,0)
60% MPD
Cryoprotected with 10% glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 294.846 α = 90 b = 294.846 β = 90 c = 99.525 γ = 120
Symmetry Space Group P 64 2 2
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 CdTe 9M 2023-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 2.78 50 99.7 0.541 0.544 0.06 0.995 9.1 78.5 64005 59.12
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 2.78 2.83 54.94 0.458 0.327 0.9
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 2.78 20.6 1.34 63529 1986 99.29 0.2283 0.2276 0.2301 0.2495 0.2522
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 6.15 f_angle_d 0.947 f_chiral_restr 0.096 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7301 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data scaling xia2 data reduction PHASER phasing