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Botulinum neurotoxin B2 binding domain in complex with human synaptotagmin I
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 8 294 0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.53 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.677 α = 90 b = 82.528 β = 90 c = 106.7 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 2019-01-27 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 2.5 106.7 99.7 0.252 0.267 0.082 0.949 5.7 11.1 18223 46.89
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 2.5 2.6 99.9 2.563 2.687 0.799 0.447 11
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 2.5 50.79 18124 1103 99.451 0.261 0.2592 0.2644 0.2834 0.2842 53.889
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] 0.157 0.595 -0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.945 r_dihedral_angle_4_deg 15.13 r_dihedral_angle_3_deg 12.976 r_dihedral_angle_1_deg 6.759 r_lrange_it 3.379 r_lrange_other 3.379 r_angle_other_deg 2.287 r_mcangle_it 2.249 r_mcangle_other 2.248 r_scangle_it 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.945 r_dihedral_angle_4_deg 15.13 r_dihedral_angle_3_deg 12.976 r_dihedral_angle_1_deg 6.759 r_lrange_it 3.379 r_lrange_other 3.379 r_angle_other_deg 2.287 r_mcangle_it 2.249 r_mcangle_other 2.248 r_scangle_it 1.602 r_scangle_other 1.602 r_mcbond_other 1.251 r_mcbond_it 1.25 r_angle_refined_deg 1.168 r_scbond_it 0.864 r_scbond_other 0.864 r_nbd_other 0.209 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.163 r_nbd_refined 0.161 r_symmetry_nbd_refined 0.135 r_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.063 r_chiral_restr 0.037 r_bond_other_d 0.035 r_symmetry_xyhbond_nbd_other 0.02 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3564 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing