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Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11
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, SITTING DROP 6.5 291 0.1 M KCl, 15 % PEG 5000 MME, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.21 α = 87.833 b = 73.276 β = 65.745 c = 76.367 γ = 66.551
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 2016-07-09 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) 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 2.32 44.58 98.6 0.997 13.9 3.9 54491 39.5066366088
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 2.32 2.39 0.484 0.484 0.81
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 2NM1 2.32005878384 37.4802763841 1.96873750686 54471 2764 98.5365412446 0.172791002619 0.17008565026 0.1726 0.22226131306 0.2234 51.9821761911
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 14.0599176743 f_angle_d 1.01813494627 f_chiral_restr 0.0450323149764 f_bond_d 0.00807835491788 f_plane_restr 0.00369490387672
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8920 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX model building XDS data reduction XDS data scaling PHASER phasing