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Botulinum neurotoxin A4 Hc domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 10 mM Spermine tetrahydrochloride,
10 mM Spermidine trihydrochloride,
10 mM 1,4-Diaminobutane dihydrochloride,
10 mM D-L-Ornithine monohydrochloride,
0.1 M MOPSO/bis-tris pH 6.5,
15%(w/v) PEG 3K,
20%(v/v) 1,2,4-butanetriol,
1%(w/v) NDSB 256
Crystal Properties Matthews coefficient Solvent content 2.56 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.888 α = 90 b = 115.888 β = 90 c = 115.888 γ = 90
Symmetry Space Group P 21 3
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 2017-04-04 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) 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 1.34 81.95 100 0.091 0.02 0.999 17.5 21.7 116165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.36 100 2.306 0.74 0.421 1.1 10.5
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 2vua 1.34 81.95 113786 2017 99.98 0.14425 0.14401 0.1442 0.15829 0.1587 RANDOM 20.807
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.928 r_sphericity_free 22.325 r_dihedral_angle_4_deg 16.119 r_sphericity_bonded 12.905 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_1_deg 6.974 r_long_range_B_refined 5.381 r_long_range_B_other 5.38 r_scangle_other 4.639 r_mcangle_other 4.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.928 r_sphericity_free 22.325 r_dihedral_angle_4_deg 16.119 r_sphericity_bonded 12.905 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_1_deg 6.974 r_long_range_B_refined 5.381 r_long_range_B_other 5.38 r_scangle_other 4.639 r_mcangle_other 4.012 r_mcangle_it 4.011 r_scbond_it 3.678 r_scbond_other 3.678 r_mcbond_it 2.973 r_mcbond_other 2.872 r_rigid_bond_restr 1.565 r_angle_refined_deg 1.49 r_angle_other_deg 0.912 r_chiral_restr 0.215 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3423 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing