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Tetanus neurotoxin mutant-(H233A/E234Q/H237A/Y375F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z7H 1Z7H, 1AF9, 5N0B experimental model PDB 1AF9 1Z7H, 1AF9, 5N0B experimental model PDB 5N0B 1Z7H, 1AF9, 5N0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M MOPS pH 7.0, 9% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.542 α = 90 b = 145.542 β = 90 c = 129.038 γ = 120
Symmetry Space Group P 31 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 EIGER X 16M 2020-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.987 SPring-8 BL44XU
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 2.27 48.28 99.2 0.126 0.137 0.053 0.997 10.7 6.6 72360 38.3
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 2.27 2.32 94.7 1.03 0.446 0.634 1.7 5.9
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1Z7H, 1AF9, 5N0B 2.27 48.28 72353 3663 99.1 0.188 0.186 0.186 0.233 0.2161 Random 59.7
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_4_deg 16.291 r_lrange_it 6.786 r_dihedral_angle_1_deg 6.294 r_scangle_it 4.37 r_mcangle_it 3.71 r_scbond_it 2.961 r_mcbond_it 2.415 r_angle_refined_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_4_deg 16.291 r_lrange_it 6.786 r_dihedral_angle_1_deg 6.294 r_scangle_it 4.37 r_mcangle_it 3.71 r_scbond_it 2.961 r_mcbond_it 2.415 r_angle_refined_deg 0.905 r_nbtor_refined 0.307 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.191 r_metal_ion_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.078 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10393 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing