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Crystal structure of SXN101959, a Clostridium botulinum neurotoxin type D derivative and targeted secretion inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289.1 0.1 M sodium actetate pH 5.5, 0.8 M sodium formate, 10 % w /v polyethylene glycol 8000, 10 % w /v polyethylene glycol 1000
Crystal Properties Matthews coefficient Solvent content 2.7 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.201 α = 90 b = 143.916 β = 90 c = 172.762 γ = 90
Symmetry Space Group P 21 21 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 2014-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.1 110 89 0.127 6 3.4 35774 35774
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.25 81.2 1.02 1 2.6
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 (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 2FPQ 3.1 110 34012 1739 87.89 0.25194 0.24969 0.2472 0.29532 0.2926 RANDOM 100.488
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] -0.56 5.38 -4.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_4_deg 9.934 r_dihedral_angle_1_deg 5.507 r_long_range_B_refined 3.357 r_long_range_B_other 3.357 r_mcangle_it 1.935 r_mcangle_other 1.935 r_mcbond_it 1.026 r_mcbond_other 1.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_4_deg 9.934 r_dihedral_angle_1_deg 5.507 r_long_range_B_refined 3.357 r_long_range_B_other 3.357 r_mcangle_it 1.935 r_mcangle_other 1.935 r_mcbond_it 1.026 r_mcbond_other 1.026 r_scangle_other 1.023 r_angle_refined_deg 0.968 r_angle_other_deg 0.829 r_scbond_it 0.468 r_scbond_other 0.468 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 13249 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing DIALS data reduction