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Botulinum neurotoxin B2 binding domain in complex with GD1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.16 M calcium acetate hydrate, 0.08 M MES pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.639 α = 90 b = 56.162 β = 121.996 c = 76.792 γ = 90
Symmetry Space Group C 1 2 1
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 2019-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 63.816 99.6 0.1 0.109 0.042 0.996 10.6 6.4 46758 16.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 96.2 0.685 0.777 0.356 0.682 2.3 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4kbb 1.8 63.73 46734 2081 99.515 0.166 0.164 0.1757 0.2032 0.2069 22.469
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] -0.72 -0.442 1.671 -0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 123.144 r_dihedral_angle_2_deg 33.614 r_dihedral_angle_4_deg 13.019 r_dihedral_angle_3_deg 12.279 r_lrange_it 9.955 r_lrange_other 9.935 r_scangle_it 8.703 r_scangle_other 8.702 r_dihedral_angle_1_deg 7.408 r_scbond_it 6.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 123.144 r_dihedral_angle_2_deg 33.614 r_dihedral_angle_4_deg 13.019 r_dihedral_angle_3_deg 12.279 r_lrange_it 9.955 r_lrange_other 9.935 r_scangle_it 8.703 r_scangle_other 8.702 r_dihedral_angle_1_deg 7.408 r_scbond_it 6.282 r_scbond_other 6.281 r_mcangle_it 4.823 r_mcangle_other 4.823 r_mcbond_it 3.894 r_mcbond_other 3.894 r_angle_other_deg 2.262 r_angle_refined_deg 1.351 r_symmetry_nbd_refined 0.257 r_nbd_other 0.251 r_symmetry_xyhbond_nbd_refined 0.241 r_symmetry_nbd_other 0.205 r_nbd_refined 0.182 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_other 0.124 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.064 r_bond_other_d 0.035 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3602 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing