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Botulinum neurotoxin subtype A6 cell binding domain in complex with GD1a ganglioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TWO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289.15 0.2 M NaCl, 0.1 M HEPES pH 7.0,
20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.307 α = 90 b = 83.636 β = 98.659 c = 58.313 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 PIXEL DECTRIS EIGER2 X 16M 2021-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 57.65 100 0.05 0.998 7.2 13.6 67218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 2.241 0.991 0.3 13.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6TWO 1.5 57.65 67156 3343 99.949 0.205 0.2033 0.2365 0.2077 0.05 27.134
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] -0.885 0.47 -0.714 1.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_4_deg 14.768 r_dihedral_angle_3_deg 12.755 r_dihedral_angle_1_deg 7.632 r_lrange_it 6.378 r_lrange_other 6.358 r_scangle_it 5.004 r_scangle_other 5.003 r_scbond_it 3.287 r_scbond_other 3.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_4_deg 14.768 r_dihedral_angle_3_deg 12.755 r_dihedral_angle_1_deg 7.632 r_lrange_it 6.378 r_lrange_other 6.358 r_scangle_it 5.004 r_scangle_other 5.003 r_scbond_it 3.287 r_scbond_other 3.287 r_mcangle_it 3.181 r_mcangle_other 3.181 r_mcbond_it 2.195 r_mcbond_other 2.188 r_angle_refined_deg 1.574 r_angle_other_deg 1.342 r_nbd_other 0.197 r_nbd_refined 0.191 r_symmetry_nbd_refined 0.184 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3402 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing