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X-ray structure of non-toxic non-hemagglutinin (NTNH) protein from botulinum neurotoxin serotype X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 15 mg/ml NTNH/X in 20 mM MES pH 5.5, 150 mM NaCl, 0.5 mM TCEP mixed in 2:1 volume ratio with 90 mM MES/imidazole pH 6.5, 9% (w/v) PEG 4,000, 18% (v/v) glycerol, and 3% (w/v) dextran sulfate sodium salt
Crystal Properties Matthews coefficient Solvent content 4.4 72.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.106 α = 90 b = 174.106 β = 90 c = 138.023 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 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 3.3 87.05 100 0.202 0.208 0.047 0.999 7 19.3 36727
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 3.3 3.45 100 2.772 2.859 0.699 0.924 16.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.3 73.74 36531 1939 99.526 0.279 0.2763 0.2859 0.3326 0.3372 220.051
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] 9.301 4.651 9.301 -30.173
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 37.622 r_lrange_it 37.621 r_mcangle_it 26.686 r_mcangle_other 26.684 r_scangle_it 26.536 r_scangle_other 26.535 r_mcbond_it 17.506 r_mcbond_other 17.506 r_scbond_it 16.783 r_scbond_other 16.782
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 37.622 r_lrange_it 37.621 r_mcangle_it 26.686 r_mcangle_other 26.684 r_scangle_it 26.536 r_scangle_other 26.535 r_mcbond_it 17.506 r_mcbond_other 17.506 r_scbond_it 16.783 r_scbond_other 16.782 r_dihedral_angle_6_deg 14.168 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 6.167 r_dihedral_angle_2_deg 3.892 r_angle_refined_deg 1.044 r_angle_other_deg 0.616 r_nbd_other 0.283 r_symmetry_nbd_refined 0.266 r_symmetry_nbd_other 0.23 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.049 r_gen_planes_other 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9710 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing