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Crystal Structure of botulinum neurotoxin A2 cell binding domain in complex with GD1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.2 M Lithium citrate tribasic tetrahydrate 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.63 66.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.068 α = 90 b = 105.068 β = 90 c = 132.58 γ = 90
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 XE 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) 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 2.1 105.07 100 0.99 11.1 27.3 83782
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.4 0.9 21.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MOY 2.1 105.068 83719 4166 99.981 0.19 0.1883 0.2264 0.1956 46.052
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] 0.747 0.747 -1.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.864 r_dihedral_angle_other_3_deg 16.632 r_dihedral_angle_3_deg 15.987 r_dihedral_angle_4_deg 15.785 r_lrange_it 8.938 r_lrange_other 8.927 r_dihedral_angle_1_deg 7.908 r_scangle_it 7.251 r_scangle_other 7.25 r_mcangle_it 5.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.864 r_dihedral_angle_other_3_deg 16.632 r_dihedral_angle_3_deg 15.987 r_dihedral_angle_4_deg 15.785 r_lrange_it 8.938 r_lrange_other 8.927 r_dihedral_angle_1_deg 7.908 r_scangle_it 7.251 r_scangle_other 7.25 r_mcangle_it 5.564 r_mcangle_other 5.564 r_scbond_it 4.878 r_scbond_other 4.877 r_mcbond_it 3.905 r_mcbond_other 3.897 r_angle_other_deg 2.272 r_angle_refined_deg 1.616 r_nbd_other 0.316 r_symmetry_nbd_other 0.217 r_nbd_refined 0.196 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.159 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.143 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.071 r_bond_other_d 0.034 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6733 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing