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Binding domain of BoNT/A6
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, HANGING DROP 289.15 0.2 M Sodium acetate trihydrate, 0.1 M Bis-Tris propane-HCl pH 7.5, 22% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.542 α = 90 b = 105.587 β = 90 c = 112.405 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-F 2018-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.35 112.41 100 0.999 10.7 10.5 104434
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 1.35 1.37 0.463 0.9
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 1.35 56.266 104032 2594 99.779 0.144 0.143 0.1437 0.1776 0.178 19.653
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] 2.757 -1.398 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.374 r_dihedral_angle_4_deg 14.824 r_dihedral_angle_3_deg 11.509 r_dihedral_angle_1_deg 7.801 r_rigid_bond_restr 5.017 r_lrange_it 3.506 r_lrange_other 3.381 r_scangle_it 2.68 r_scangle_other 2.679 r_mcangle_other 2.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.374 r_dihedral_angle_4_deg 14.824 r_dihedral_angle_3_deg 11.509 r_dihedral_angle_1_deg 7.801 r_rigid_bond_restr 5.017 r_lrange_it 3.506 r_lrange_other 3.381 r_scangle_it 2.68 r_scangle_other 2.679 r_mcangle_other 2.296 r_mcangle_it 2.295 r_scbond_it 2.096 r_scbond_other 2.096 r_angle_refined_deg 1.743 r_mcbond_it 1.732 r_mcbond_other 1.729 r_angle_other_deg 1.495 r_symmetry_xyhbond_nbd_refined 0.358 r_symmetry_nbd_refined 0.229 r_nbd_refined 0.222 r_nbd_other 0.203 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_other 0.116 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3448 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing