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Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with a Novel Cyclic Peptide Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 25% PEG 3350, BIs-Tris and Lithium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.889 α = 90 b = 66.367 β = 98.51 c = 64.863 γ = 90
Symmetry Space Group P 1 21 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 2012-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.94 50 91.8 0.136 9.3 12.5 28926
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.02 59.3 0.45 1.5 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3BWI 1.94 42.83 27451 1461 91.3 0.18 0.177 0.1874 0.229 0.2365 RANDOM 32.47
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] 5.08 1.13 -2.44 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.376 r_dihedral_angle_3_deg 15.542 r_dihedral_angle_4_deg 14.454 r_dihedral_angle_1_deg 6.936 r_angle_refined_deg 1.867 r_angle_other_deg 0.929 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.376 r_dihedral_angle_3_deg 15.542 r_dihedral_angle_4_deg 14.454 r_dihedral_angle_1_deg 6.936 r_angle_refined_deg 1.867 r_angle_other_deg 0.929 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3441 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing