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Crystal structure of the tetanus neurotoxin in complex with GD1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z7H 1Z7H, 1FV2 experimental model PDB 1FV2 1Z7H, 1FV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% v/v polyethylene glycol 3350, 0.1M Bis-Tris propane pH 6.5, 0.2M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.2 61.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.695 α = 90 b = 136.84 β = 90.07 c = 92.63 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 PILATUS 6M-F 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 2.6 68.5 99.8 0.134 0.088 0.996 10 6.3 58411
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 2.6 2.86 99.9 0.937 0.644 0.307 6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1Z7H, 1FV2 2.6 68.5 55548 2862 99.83 0.20505 0.20288 0.2079 0.24723 0.2491 RANDOM 64.736
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] 1.7 2.87 -0.59 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_4_deg 13.096 r_dihedral_angle_3_deg 13.016 r_long_range_B_refined 6.527 r_long_range_B_other 6.524 r_dihedral_angle_1_deg 6.086 r_mcangle_it 4.246 r_mcangle_other 4.246 r_scangle_other 3.776 r_mcbond_it 2.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_4_deg 13.096 r_dihedral_angle_3_deg 13.016 r_long_range_B_refined 6.527 r_long_range_B_other 6.524 r_dihedral_angle_1_deg 6.086 r_mcangle_it 4.246 r_mcangle_other 4.246 r_scangle_other 3.776 r_mcbond_it 2.449 r_mcbond_other 2.449 r_scbond_it 2.173 r_scbond_other 2.173 r_angle_refined_deg 1.17 r_angle_other_deg 0.874 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10348 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing