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Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EPW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 0.2 M magnesium chloride, Tris pH 7.0, 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.5 65.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.6 α = 90 b = 211.05 β = 90 c = 120.32 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 PIXEL DECTRIS PILATUS 6M-F 2016-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 57.5 99.9 0.113 0.134 0.071 0.998 9.8 6.6 142330
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.9 1.399 1.652 0.866 0.499 6.7
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 MOLECULAR REPLACEMENT THROUGHOUT 1EPW 2 57.5 135070 7218 99.91 0.19133 0.18962 0.1965 0.22339 0.2266 RANDOM 44.844
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] 1.61 -2.65 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_4_deg 16.206 r_dihedral_angle_3_deg 13.346 r_long_range_B_refined 7.055 r_long_range_B_other 6.99 r_dihedral_angle_1_deg 6.271 r_scangle_other 4.738 r_mcangle_it 4.068 r_mcangle_other 4.068 r_scbond_it 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_4_deg 16.206 r_dihedral_angle_3_deg 13.346 r_long_range_B_refined 7.055 r_long_range_B_other 6.99 r_dihedral_angle_1_deg 6.271 r_scangle_other 4.738 r_mcangle_it 4.068 r_mcangle_other 4.068 r_scbond_it 2.92 r_scbond_other 2.917 r_mcbond_it 2.556 r_mcbond_other 2.556 r_angle_refined_deg 1.251 r_angle_other_deg 0.729 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10673 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing