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Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.15 M Ammonium sulfate, 14% PEG 4000, 0.1 M Hepes (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.086 α = 90 b = 49.877 β = 101.037 c = 133.508 γ = 90
Symmetry Space Group P 1 2 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 2017-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 131.04 96.3 0.093 0.993 6.3 2.8 43226 62.07
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 2.5 2.59 0.684 0.661
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 3ffz 2.5 70.42 1.33 41851 3755 89.71 0.2271 0.2264 0.2316 0.2411 0.2405 70.1
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 16.6345 f_angle_d 0.7976 f_chiral_restr 0.0516 f_bond_d 0.0066 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7287 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 16
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement PHASER phasing Coot model building iMOSFLM data reduction Aimless data scaling