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HA1 subcomponent of botulinum type C progenitor toxin complexed with N-acetylneuramic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12% ethanol, 1.7M sodium chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.32 α = 90 b = 61.722 β = 104.28 c = 82.397 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 CCD ADSC QUANTUM 4 2006-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 50 95 0.05 3.3 32592 32591 22.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 88.7 0.269 5 3.1 3038
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 1QXM 2.2 46.05 32591 3249 94.8 0.205 0.205 0.2049 0.255 0.2544 RANDOM 28.9
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] -4.23 -2.19 2.68 1.55
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_improper_angle_d 2.83 c_scangle_it 2.74 c_mcangle_it 2.37 c_scbond_it 1.92 c_mcbond_it 1.45 c_angle_deg 1.2 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_improper_angle_d 2.83 c_scangle_it 2.74 c_mcangle_it 2.37 c_scbond_it 1.92 c_mcbond_it 1.45 c_angle_deg 1.2 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4763 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 63
Software Software Software Name Purpose ADSC data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing