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Botulinum neurotoxin A3 Hc domain in complex with GD1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 289.15 0.1 M Sodium acetate, 22% v/v PEG Smear broad (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000)
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.228 α = 90 b = 73.129 β = 90 c = 140.18 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 EIGER2 XE 16M 2019-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92 Diamond I04
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 1.75 140.18 99.8 0.217 0.06 0.996 11.2 26.1 47739
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 1.75 1.78 100 2.99 0.91 0.75 1.5 22.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6f0o 1.75 70.09 47659 1904 99.703 0.18 0.1784 0.2129 0.2046 24.222
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] -0.77 1.447 -0.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 50.641 r_dihedral_angle_2_deg 34.529 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 13.592 r_dihedral_angle_1_deg 7.858 r_lrange_it 6.395 r_lrange_other 6.395 r_scangle_it 4.923 r_scangle_other 4.922 r_scbond_it 3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 50.641 r_dihedral_angle_2_deg 34.529 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 13.592 r_dihedral_angle_1_deg 7.858 r_lrange_it 6.395 r_lrange_other 6.395 r_scangle_it 4.923 r_scangle_other 4.922 r_scbond_it 3.22 r_scbond_other 3.22 r_mcangle_it 3.2 r_mcangle_other 3.2 r_angle_other_deg 2.496 r_mcbond_it 2.131 r_mcbond_other 2.127 r_angle_refined_deg 1.654 r_nbd_other 0.237 r_symmetry_nbd_refined 0.216 r_symmetry_nbd_other 0.214 r_nbd_refined 0.193 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.137 r_symmetry_xyhbond_nbd_other 0.123 r_symmetry_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.082 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3357 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing