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Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 166-174 stretch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ELC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 protein complex - 6 microL LCA C134S at 145 microM + 1.4 microL KG23 at 1.25 milli-M, Reservoir - 17.5% PEG 600, 0.065 M HEPES pH 7.5. Cryoprotectant - CryoProtX CM1, 10% PEG 20K, 100 milliM CHC (citric acid, HEPES, CHES - 40% pH 4 / 60% pH 10), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.634 α = 90 b = 65.634 β = 90 c = 201.725 γ = 90
Symmetry Space Group P 43 21 2
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 315r mirrors 2011-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97240 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.79 50 99.2 0.377 0.365 9.79 15.4 42673 42323 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.9 94.9 4.886 4.726 0.86 15.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 4ELC 1.93 62.41 42323 32454 1724 99.96 0.19561 0.19255 0.1908 0.25199 0.2513 RANDOM 26.766
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] -0.09 -0.09 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.606 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_4_deg 13.167 r_dihedral_angle_1_deg 6.166 r_scangle_it 5.592 r_scbond_it 3.786 r_mcangle_it 2.691 r_mcbond_it 1.731 r_angle_refined_deg 1.514 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.606 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_4_deg 13.167 r_dihedral_angle_1_deg 6.166 r_scangle_it 5.592 r_scbond_it 3.786 r_mcangle_it 2.691 r_mcbond_it 1.731 r_angle_refined_deg 1.514 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3502 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 53
Software Software Software Name Purpose DNA data collection REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling REFMAC phasing