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Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 297 0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 4.98 75.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.415 α = 90 b = 351.971 β = 90 c = 101.968 γ = 90
Symmetry Space Group C 2 2 21
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 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 1.00 SSRL BL1-5
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 2.62 40 90.04 0.085 4.5 92718 2 2
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 2.62 2.71 71 0.476
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1s0e 2.62 40 1.5 79045 83222 4177 90.04 0.1881 0.18807 0.18601 0.1906 0.22733 0.2304 RANDOM 38.371
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] 5.22 -1.75 -3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.632 r_dihedral_angle_3_deg 17.645 r_dihedral_angle_4_deg 17.464 r_dihedral_angle_1_deg 8.512 r_scangle_it 2.274 r_angle_refined_deg 1.499 r_scbond_it 1.452 r_mcangle_it 1.05 r_angle_other_deg 0.934 r_mcbond_it 0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.632 r_dihedral_angle_3_deg 17.645 r_dihedral_angle_4_deg 17.464 r_dihedral_angle_1_deg 8.512 r_scangle_it 2.274 r_angle_refined_deg 1.499 r_scbond_it 1.452 r_mcangle_it 1.05 r_angle_other_deg 0.934 r_mcbond_it 0.626 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.217 r_nbtor_refined 0.198 r_symmetry_vdw_other 0.196 r_nbd_other 0.194 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.116 r_mcbond_other 0.094 r_nbtor_other 0.091 r_metal_ion_refined 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10771 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing