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Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 15 % PEG 20000 and 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.23 61.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.147 α = 90 b = 223.147 β = 90 c = 58.491 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 CCD ADSC QUANTUM 315 2015-10-11 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 2.2 111.57 99.2 0.096 0.076 0.994 10.2 4.9 84263 33.7319682932
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 2.2 2.24 0.722 0.565 0.733
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2NM1 2.20001465977 96.6254853891 1.33786967781 84236 4213 99.0440804713 0.195082532664 0.194221152895 0.211016532578 0.212 46.2212800912
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 12.698630576 f_angle_d 1.12011630159 f_chiral_restr 0.0537142764745 f_bond_d 0.00819009759985 f_plane_restr 0.00569050369452
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9143 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction Aimless data scaling Coot model building