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Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289.15 0.1 M SPG (succinic acid, sodium phosphate monobasic monohydrate, and glycine) buffer pH 7.0, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.894 α = 90 b = 143.894 β = 90 c = 51.695 γ = 90
Symmetry Space Group P 42 21 2
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 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 2 143.89 100 0.129 0.134 0.036 1 13.2 26.3 37319
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 2.05 3.807 3.952 1.06 0.626 26.6
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 (All) 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 2 64.434 37257 1882 99.944 0.19 0.1883 0.1889 0.2237 0.2248 RANDOM 55.903
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] 1.266 1.266 -2.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.226 r_dihedral_angle_6_deg 16.232 r_dihedral_angle_2_deg 15.224 r_lrange_it 8.207 r_lrange_other 8.207 r_dihedral_angle_1_deg 7.449 r_scangle_it 6.671 r_scangle_other 6.67 r_mcangle_it 5.27 r_mcangle_other 5.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.226 r_dihedral_angle_6_deg 16.232 r_dihedral_angle_2_deg 15.224 r_lrange_it 8.207 r_lrange_other 8.207 r_dihedral_angle_1_deg 7.449 r_scangle_it 6.671 r_scangle_other 6.67 r_mcangle_it 5.27 r_mcangle_other 5.269 r_scbond_it 4.904 r_scbond_other 4.903 r_mcbond_it 3.912 r_mcbond_other 3.912 r_angle_refined_deg 1.91 r_angle_other_deg 0.606 r_nbd_refined 0.226 r_metal_ion_refined 0.208 r_symmetry_nbd_other 0.197 r_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3218 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing