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Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLK-G12
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 0.2 M ammonium sulfate, 14 % PEG 8000, 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.58 65.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.24 α = 90 b = 53.1899 β = 92.35 c = 114.41 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 PIXEL DECTRIS PILATUS 6M 2016-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.9 38.28 96.7 0.12 0.12 0.964 7.4 3.2 20044 53.409365795
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 2.9 3.08 0.611 0.61 0.684
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 2.90008139771 38.2777810241 1.35003060314 20026 1029 96.2048424289 0.214808450038 0.212482169622 0.2178 0.257539668402 0.2567 47.2824239641
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 13.1941537435 f_angle_d 0.696667963864 f_chiral_restr 0.0292863390444 f_bond_d 0.00396326196993 f_plane_restr 0.00277876611449
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4579 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing