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Structure of the binding domain of BoNT/A mutant H1253K in complex with the GM1a ganglioside receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M PCTP pH 5.0, 25 % w/v PEG 1500
(PACT C2)
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.437 α = 90 b = 114.512 β = 90 c = 106.409 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 2017-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968 Diamond I24
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 1.6 61.82 99.9 0.055 0.064 0.032 0.999 15.6 7.1 59267
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 1.6 1.64 99.6 1.327 1.541 0.772 0.783 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 61.82 56364 2862 99.76 0.1728 0.17161 0.1826 0.19653 0.2049 RANDOM 27.716
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] 0.89 -0.05 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.514 r_dihedral_angle_4_deg 20.753 r_dihedral_angle_3_deg 12.489 r_dihedral_angle_1_deg 7.032 r_long_range_B_refined 5.603 r_long_range_B_other 5.338 r_scangle_other 2.785 r_mcangle_it 2.012 r_mcangle_other 2.012 r_scbond_it 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.514 r_dihedral_angle_4_deg 20.753 r_dihedral_angle_3_deg 12.489 r_dihedral_angle_1_deg 7.032 r_long_range_B_refined 5.603 r_long_range_B_other 5.338 r_scangle_other 2.785 r_mcangle_it 2.012 r_mcangle_other 2.012 r_scbond_it 1.74 r_scbond_other 1.74 r_angle_refined_deg 1.56 r_mcbond_it 1.223 r_mcbond_other 1.222 r_angle_other_deg 0.936 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3449 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing