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Crystal Structure of BoNT/A-LCHn domain in complex with VNA ciA-D12/11/ciA-B5 and VHH ciA-H7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 291 13 % PEG 20000, 0.1 M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.96 58.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.288 α = 90 b = 90.253 β = 119.037 c = 144.771 γ = 90
Symmetry Space Group C 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 CCD ADSC QUANTUM 315 2015-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.02 47.21 99.8 0.094 0.09 0.995 9.8 3.7 103999 26.8751899906
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.05 0.716 0.678 0.648
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 3V0A 2.02000221988 47.2074892055 1.33645969424 103988 5185 99.7104228593 0.183342226535 0.182756746715 0.1848 0.194475502331 0.1939 37.4504074541
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 14.0703242635 f_angle_d 1.44637882083 f_chiral_restr 0.073588937312 f_bond_d 0.0155596598749 f_plane_restr 0.00791720281227
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9562 Nucleic Acid Atoms Solvent Atoms 799 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction Coot model building PHASER phasing