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Binding domain of BoNT/A5
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 289.15 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Sodium potassium tartrate tetrahydrate, 0.1 M Sodium oxamate, 0.1 M Imidazole, 0.1 M 2-[N-morpholino]ethanesulfonic acid, pH 6.5, 10% v/v Ethylene glycol, 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.547 α = 90 b = 60.266 β = 90 c = 185.147 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 PILATUS3 6M 2018-07-07 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) 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 1.15 92.57 100 0.998 11.9 12.1 173797
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 1.15 1.17 99.5 0.447 1.9 10
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2VUA 1.15 92.57 173516 3494 99.881 0.136 0.1351 0.1356 0.1612 0.1608 16.536
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] 0.259 -1.65 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.718 r_dihedral_angle_4_deg 19.386 r_dihedral_angle_3_deg 12.207 r_dihedral_angle_other_3_deg 8.231 r_dihedral_angle_1_deg 7.606 r_rigid_bond_restr 6.027 r_scangle_it 4.286 r_scangle_other 4.285 r_lrange_it 4.285 r_lrange_other 4.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.718 r_dihedral_angle_4_deg 19.386 r_dihedral_angle_3_deg 12.207 r_dihedral_angle_other_3_deg 8.231 r_dihedral_angle_1_deg 7.606 r_rigid_bond_restr 6.027 r_scangle_it 4.286 r_scangle_other 4.285 r_lrange_it 4.285 r_lrange_other 4.012 r_scbond_it 3.79 r_scbond_other 3.788 r_mcangle_other 2.477 r_mcangle_it 2.474 r_angle_refined_deg 2.202 r_mcbond_it 1.956 r_mcbond_other 1.923 r_angle_other_deg 1.626 r_chiral_restr_other 0.348 r_nbd_refined 0.285 r_symmetry_nbd_refined 0.272 r_xyhbond_nbd_refined 0.264 r_symmetry_nbd_other 0.216 r_symmetry_xyhbond_nbd_other 0.212 r_symmetry_xyhbond_nbd_refined 0.196 r_nbd_other 0.186 r_nbtor_refined 0.182 r_chiral_restr 0.125 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3416 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing