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Crystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 0.1 M MES pH 6.0,
0.2 M CaCl2
20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.908 α = 101.71 b = 105.208 β = 90 c = 179.621 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 PILATUS3 6M 2018-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
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 58.63 97.1 0.09 0.11 0.06 0.99 6.74 3.6 531729
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 1.6 1.63 95.2 0.472 3.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.6 58.63 505114 26608 97.05 0.15328 0.15074 0.1558 0.20169 0.2057 RANDOM 28.266
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] 2.37 -0.75 1.41 -0.22 -1.66 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.563 r_dihedral_angle_4_deg 17.386 r_dihedral_angle_3_deg 12.443 r_rigid_bond_restr 10.856 r_dihedral_angle_1_deg 6.328 r_long_range_B_refined 6.05 r_long_range_B_other 5.675 r_scangle_other 4.677 r_scbond_it 3.818 r_scbond_other 3.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.563 r_dihedral_angle_4_deg 17.386 r_dihedral_angle_3_deg 12.443 r_rigid_bond_restr 10.856 r_dihedral_angle_1_deg 6.328 r_long_range_B_refined 6.05 r_long_range_B_other 5.675 r_scangle_other 4.677 r_scbond_it 3.818 r_scbond_other 3.814 r_mcangle_it 3.728 r_mcangle_other 3.728 r_mcbond_it 2.859 r_mcbond_other 2.859 r_angle_other_deg 1.461 r_angle_refined_deg 1.378 r_chiral_restr 0.066 r_bond_other_d 0.012 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29021 Nucleic Acid Atoms Solvent Atoms 3415 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing